Not sure if anyone else got problems with this, but I tried authoring an AVCHD-USB version of v2.5 to play on my PS3 and because of the error where that glitch occurs, TSMuxer.exe crashes and it was unable to do it.
I also tried remuxing the MKV using MKVExtractGUI2 and mkvmerge and they both didn't go right too.
So has anyone else managed to remux it?