Mike, the problem is still going on. I tested with two different Blu-rays, from Batman.
Here's a new dump: 
http://mandandoprohd2.minus.com/mAyoZsFi0/
It's affecting all extra features. Again, the 3:2 Aspect Ratio. This one is from the theatrical trailer.
Note: The Blu-ray tested for this dump is Batman Returns (1992).
I also saw these messages while trying to open the Blu-ray, located in my external Hard Drive from Western Digital:
This is a MyBoook Essential External Hard Drive.
Despite this message, and this one:
I was able to save all extra features. However, I didn't tried with the movie. Instead, I used TSMuxer + MKVToolnix to do this task. And I will have to do this with the extra features if the bug is not fixed.
P.S. Specs from this theatrical trailer, taken from the m2ts file:
General
ID                             : 0 (0x0)
Complete name                  : R:\Blu-rays\Batman - O Retorno (1992)\Batman Returns (1992)\BDMV\STREAM\00090.m2ts
Format                         : BDAV
Format/Info                    : Blu-ray Video
File size                      : 144 MiB
Duration                       : 2mn 35s
Overall bit rate               : 7 745 Kbps
Maximum Overall bit rate       : 48.0 Mbps
Video
ID                             : 4113 (0x1011)
Menu ID                        : 1 (0x1)
Format                         : VC-1
Format profile                 : Advanced@L2
Codec ID                       : 234
Duration                       : 2mn 35s
Bit rate                       : 5 447 Kbps
Width                          : 720 pixels
Height                         : 480 pixels
Display aspect ratio           : 16:9
Frame rate                     : 29.970 fps
Standard                       : NTSC
Chroma subsampling             : 4:2:0
Bit depth                      : 8 bits
Scan type                      : Interlaced
Scan order                     : Bottom Field First
Compression mode               : Lossy
Bits/(Pixel*Frame)             : 0.526
Stream size                    : 101 MiB (70%)
Audio #1
ID                             : 4352 (0x1100)
Menu ID                        : 1 (0x1)
Format                         : AC-3
Format/Info                    : Audio Coding 3
Format profile                 : Dolby Digital
Mode extension                 : CM (complete main)
Format settings, Endianness    : Big
Codec ID                       : 129
Duration                       : 2mn 35s
Bit rate mode                  : Constant
Bit rate                       : 192 Kbps
Channel(s)                     : 2 channels
Channel positions              : Front: L R
Sampling rate                  : 48.0 KHz
Bit depth                      : 16 bits
Compression mode               : Lossy
Stream size                    : 3.57 MiB (2%)
Audio #2
ID                             : 4353 (0x1101)
Menu ID                        : 1 (0x1)
Format                         : AC-3
Format/Info                    : Audio Coding 3
Format profile                 : Dolby Digital
Mode extension                 : CM (complete main)
Format settings, Endianness    : Big
Codec ID                       : 129
Duration                       : 2mn 35s
Bit rate mode                  : Constant
Bit rate                       : 192 Kbps
Channel(s)                     : 2 channels
Channel positions              : Front: L R
Sampling rate                  : 48.0 KHz
Bit depth                      : 16 bits
Compression mode               : Lossy
Stream size                    : 3.57 MiB (2%)
Audio #3
ID                             : 4354 (0x1102)
Menu ID                        : 1 (0x1)
Format                         : AC-3
Format/Info                    : Audio Coding 3
Format profile                 : Dolby Digital
Mode extension                 : CM (complete main)
Format settings, Endianness    : Big
Codec ID                       : 129
Duration                       : 2mn 35s
Bit rate mode                  : Constant
Bit rate                       : 192 Kbps
Channel(s)                     : 2 channels
Channel positions              : Front: L R
Sampling rate                  : 48.0 KHz
Bit depth                      : 16 bits
Compression mode               : Lossy
Stream size                    : 3.57 MiB (2%)
Audio #4
ID                             : 4355 (0x1103)
Menu ID                        : 1 (0x1)
Format                         : AC-3
Format/Info                    : Audio Coding 3
Format profile                 : Dolby Digital
Mode extension                 : CM (complete main)
Format settings, Endianness    : Big
Codec ID                       : 129
Duration                       : 2mn 35s
Bit rate mode                  : Constant
Bit rate                       : 192 Kbps
Channel(s)                     : 2 channels
Channel positions              : Front: L R
Sampling rate                  : 48.0 KHz
Bit depth                      : 16 bits
Compression mode               : Lossy
Stream size                    : 3.57 MiB (2%)
Audio #5
ID                             : 4356 (0x1104)
Menu ID                        : 1 (0x1)
Format                         : AC-3
Format/Info                    : Audio Coding 3
Format profile                 : Dolby Digital
Mode extension                 : CM (complete main)
Format settings, Endianness    : Big
Codec ID                       : 129
Duration                       : 2mn 35s
Bit rate mode                  : Constant
Bit rate                       : 192 Kbps
Channel(s)                     : 2 channels
Channel positions              : Front: L R
Sampling rate                  : 48.0 KHz
Bit depth                      : 16 bits
Compression mode               : Lossy
Stream size                    : 3.57 MiB (2%)
Audio #6
ID                             : 4357 (0x1105)
Menu ID                        : 1 (0x1)
Format                         : AC-3
Format/Info                    : Audio Coding 3
Format profile                 : Dolby Digital
Mode extension                 : CM (complete main)
Format settings, Endianness    : Big
Codec ID                       : 129
Duration                       : 2mn 35s
Bit rate mode                  : Constant
Bit rate                       : 192 Kbps
Channel(s)                     : 2 channels
Channel positions              : Front: L R
Sampling rate                  : 48.0 KHz
Bit depth                      : 16 bits
Compression mode               : Lossy
Stream size                    : 3.57 MiB (2%)
Audio #7
ID                             : 4358 (0x1106)
Menu ID                        : 1 (0x1)
Format                         : AC-3
Format/Info                    : Audio Coding 3
Format profile                 : Dolby Digital
Mode extension                 : CM (complete main)
Format settings, Endianness    : Big
Codec ID                       : 129
Duration                       : 2mn 35s
Bit rate mode                  : Constant
Bit rate                       : 192 Kbps
Channel(s)                     : 2 channels
Channel positions              : Front: L R
Sampling rate                  : 48.0 KHz
Bit depth                      : 16 bits
Compression mode               : Lossy
Stream size                    : 3.57 MiB (2%)
Audio #8
ID                             : 4359 (0x1107)
Menu ID                        : 1 (0x1)
Format                         : AC-3
Format/Info                    : Audio Coding 3
Format profile                 : Dolby Digital
Mode extension                 : CM (complete main)
Format settings, Endianness    : Big
Codec ID                       : 129
Duration                       : 2mn 35s
Bit rate mode                  : Constant
Bit rate                       : 192 Kbps
Channel(s)                     : 2 channels
Channel positions              : Front: L R
Sampling rate                  : 48.0 KHz
Bit depth                      : 16 bits
Compression mode               : Lossy
Stream size                    : 3.57 MiB (2%)
Audio #9
ID                             : 4360 (0x1108)
Menu ID                        : 1 (0x1)
Format                         : AC-3
Format/Info                    : Audio Coding 3
Format profile                 : Dolby Digital
Mode extension                 : CM (complete main)
Format settings, Endianness    : Big
Codec ID                       : 129
Duration                       : 2mn 35s
Bit rate mode                  : Constant
Bit rate                       : 192 Kbps
Channel(s)                     : 2 channels
Channel positions              : Front: L R
Sampling rate                  : 48.0 KHz
Bit depth                      : 16 bits
Compression mode               : Lossy
Stream size                    : 3.57 MiB (2%)
Audio #10
ID                             : 4361 (0x1109)
Menu ID                        : 1 (0x1)
Format                         : AC-3
Format/Info                    : Audio Coding 3
Format profile                 : Dolby Digital
Mode extension                 : CM (complete main)
Format settings, Endianness    : Big
Codec ID                       : 129
Duration                       : 2mn 35s
Bit rate mode                  : Constant
Bit rate                       : 192 Kbps
Channel(s)                     : 2 channels
Channel positions              : Front: L R
Sampling rate                  : 48.0 KHz
Bit depth                      : 16 bits
Compression mode               : Lossy
Stream size                    : 3.57 MiB (2%)
Text #1
ID                             : 4608 (0x1200)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #2
ID                             : 4609 (0x1201)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #3
ID                             : 4610 (0x1202)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #4
ID                             : 4611 (0x1203)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #5
ID                             : 4612 (0x1204)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #6
ID                             : 4613 (0x1205)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #7
ID                             : 4614 (0x1206)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #8
ID                             : 4615 (0x1207)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #9
ID                             : 4616 (0x1208)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #10
ID                             : 4617 (0x1209)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #11
ID                             : 4618 (0x120A)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #12
ID                             : 4619 (0x120B)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Duration                       : 2mn 17s
Delay relative to video        : 8s 642ms
Text #13
ID                             : 4620 (0x120C)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #14
ID                             : 4621 (0x120D)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #15
ID                             : 4622 (0x120E)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #16
ID                             : 4623 (0x120F)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #17
ID                             : 4624 (0x1210)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #18
ID                             : 4625 (0x1211)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #19
ID                             : 4626 (0x1212)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #20
ID                             : 4627 (0x1213)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #21
ID                             : 4628 (0x1214)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Text #22
ID                             : 4629 (0x1215)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Duration                       : 2mn 17s
Delay relative to video        : 8s 642ms
Text #23
ID                             : 4630 (0x1216)
Menu ID                        : 1 (0x1)
Format                         : PGS
Codec ID                       : 144
Delay relative to video        : 1s 1ms
Please note this is a 16:9 SD video.
You need to instruct MakeMKV to never create a Matroska file with this setting:
Display aspect ratio           : 3:2
When the Matroska file is created this way, MediaInfo reports:
Display aspect ratio           : 3:2
Original display aspect ratio  : 16:9
However, it should only report this:
Display aspect ratio           : 16:9