Broken PGS subtitle timestamps
Does MKVToolnix (v42.0) change subtitles timestamps when importing from MPLS files? For one source I got a subtitle displaying for over 2 hours instead of 9,468s (this is still long but accurate). Demuxing the subtitle track first from the source with tsMuxer and adding it as a second input file solved the problem.
Interestingly demuxing from the MKV with the broken subtitles resulted in a display duration of the same subtitle of 5,000s.