Then it sounds like a long, involved job to fix that for Avidemux. I have my hands full with DGAVCDecode. If it was just a little problem in the M2TS parsing that would be another matter, although I note that all the M2TS parsing hacks in there are prefixed with "FIXME" comments.
Soon I will release source code for DGAVCDec, at which point the method for indexing and random access of AVC will be available for re-use. The biggest complication is ensuring that the needed SPS/PPS's are available and injected when needed.