Audible "pop" in TrueHD track remux on some UHD disks

[domy94]

When remuxing certain UHD disks (examples below), the resulting .mkv file always has one or more audible pops at the same spot. Those spots are always where two blu-ray segments are spliced together (i.e. during a cut between segment A and segment B). It doesn't happen between _all_ segments, only some (most of the time, only one).

For example, when ripping the Finding Nemo UHD disc (afaik it's the US one), playlist 00800, the output file's TrueHD track has a pop at 1:32:43.5 (roughly frame 133,390) which is exactly between segments 59 and 60, and it's the 4th segment transition.

Other audio tracks are not affected, only the Dolby TrueHD one (not sure if Atmos plays a role).

mpv, VLC, MPC-BE, and Infuse Pro on the Apple TV 4K all emit the audible pop when playing the remuxed mkv.
When playing the backupped disc via VLC, the issues does not occur.
Plex on Apple TV 4K (using the default player, not the experimental one) transcodes the TrueHD track, and the issue doesn't present in the transcoded audio stream.

If I try to reencode the remuxed TrueHD stream to FLAC with eac3to (v3.3.4) myself, it spits out this error when it reaches the spot at 92%:

Code: Select all

...
process: 4%
[truehd @ 03252fa0] End of stream indicated.
[truehd @ 03252fa0] Lossless check failed - expected 82, calculated 4e.
process: 5%
[truehd @ 03252fa0] End of stream indicated.
[truehd @ 03252fa0] Lossless check failed - expected 00, calculated a2.
process: 6%
...
process: 92%
[truehd @ 03252fa0] End of stream indicated.
[truehd @ 03252fa0] Lossless check failed - expected 87, calculated 69.
[truehd @ 03252fa0] End of stream indicated.
a01 The libav decoder reported error -1094995529 while decoding.
Aborted at file position 4853858304.

I've only ever noticed this with the recent Pixar/Disney Animation UHD releases. Some other examples of the exact same issue:
- Cars (2006) at around 0:06:48 (with two minor ones later in the movie, but can't remember anymore)
- Ratatouille (2007) at around 1:16:44
- Wreck-It Ralph (2012) at around 1:25:27

I'm pretty sure there's more, but those are the ones I've watched and noticed it in so far.

Am I correct in assuming that this is a MakeMKV issue, and not a player/playback problem? If so, are the remuxed TrueHD streams irreperably broken, or can they be fixed somehow? Are there perhaps any MakeMKV settings I can play with that might make a difference?

EDIT: The debug output of MakeMKV for the Finding Nemo UHD disc: https://pastebin.com/WbqX1JAz