deho said:

The subtitles are in srt format, but the flashing is exactly what I've experienced.

Actually the muxer (tsmuxer or mkvmerge) just converts the SRT files into a BD-SUP file on-the-fly and you never see it, so the muxer is the software creating a bad BD-SUP file. No problem though--you can just demux the results to get the actual BD-SUP file it created. Then import/export the file in BDSupEdit, and then remux the whole thing again, only this time mux your fixed BD-SUP file instead of the SRT file.

Er, I think... ;)