Just thinking about the PGS subtitles that makemkv will happily mux in to a MKV. Support for PGS subs within a MKV is (in my extensive testing) non-existant in any type of player that I have found, both software and hardware (tvix, wdtv, popcornhour). I've only found one PC based software player that will even display the PGS subtitles in a .m2ts or .ts file (and this also didn't play from a MKV).
Seems when people realise this they have to go demux the MKV to get them out and put back a SRT or something in its place.
Perhaps when using a blu-ray or a m2ts with faked clpi
as source some sort of warning should be made about this or just don't allow the PGS subtitle streams to be selected?