www.makemkv.com

Chuck: Season 2 have all the episodes merged together into 1 episode in MakeMKV.
MakeMKV maps all the episodes together in the Segment map. All the episodes are seperate files on the actual blu-ray disc.

I have backed up the discs and removed the *.m2ts files and uploaded it here:
https://drive.google.com/open?id=0BypG0 ... XgxeHN6YW8

CHUCK_SEASON_2_DISC_1
Name: Chuck Season 2 Disc 1 (English)
Source file name: 00001.mpls
Duration: 4:19:54
Chapters count: 43
Size: 36.8 GB
Segment count: 6
Segment map: 6,16,7,18,8,20
File name: Chuck_Season_2_Disc_1_t00.mkv

CHUCK_SEASON_2_DISC_2
Name: Chuck Season 2 Disc 2 (English)
Source file name: 00001.mpls
Duration: 4:16:55
Chapters count: 44
Size: 37.2 GB
Segment count: 6
Segment map: 16,7,8,18,1,6
File name: Chuck_Season_2_Disc_2_t00.mkv

CHUCK_SEASON_2_DISC_3
Name: Chuck Season 2 Disc 3 (English)
Source file name: 00001.mpls
Duration: 4:18:07
Chapters count: 43
Size: 36.6 GB
Segment count: 6
Segment map: 14,6,16,7,18,1
File name: Chuck_Season_2_Disc_3_t00.mkv

CHUCK_SEASON_2_DISC_4
Name: Chuck Season 2 (English)
Source file name: 00001.mpls
Duration: 2:52:11
Chapters count: 32
Size: 24.0 GB
Segment count: 4
Segment map: 6,16,7,18
File name: Chuck_Season_2_t01.mkv

Update: Just tried the new build, MakeMKV v1.10.2 (11.9.2016 ) - and the issue still occurs.
Could you fix this please? You fixed it for Weeds Season 1.

The issue still occurs in 1.10.4 but you can split the track up yourself fairly easily.

Using MKVToolnix, drag&drop the large file from disc 1. You can leave all the settings alone but we need to setup the output to be split: go to Output tab -> "Splitting" Section -> "Split Mode" = "Before Chapters" -> Chapter #s

Set the chapter numbers for disc 1 to "8,15,22,29,36". I had to do a little trial and error to get this right, not sure why the first chapter is off-by-one. Then at the bottom you can click the button to start the job. The chapter markers for all the chapters are:

Disc 1: 8,15,22,29,36
Disc 2: 9,17,24,31,38
Disc 3: 8,15,22,30,37
Disc 4: 9,17,25

Good luck.

altano wrote:The issue still occurs in 1.10.4 but you can split the track up yourself fairly easily.

Using MKVToolnix, drag&drop the large file from disc 1. You can leave all the settings alone but we need to setup the output to be split: go to Output tab -> "Splitting" Section -> "Split Mode" = "Before Chapters" -> Chapter #s

Set the chapter numbers for disc 1 to "8,15,22,29,36". I had to do a little trial and error to get this right, not sure why the first chapter is off-by-one. Then at the bottom you can click the button to start the job. The chapter markers for all the chapters are:

Disc 1: 8,15,22,29,36
Disc 2: 9,17,24,31,38
Disc 3: 8,15,22,30,37
Disc 4: 9,17,25

Good luck.

@altano - You are my hero. Thanks so much for posting this!