If you open TMPGenc Tools and try to demux your stream, probably you'll find that there is a third stream (padding stream) besides the audio and video streams. This stream takes into account the dropped frames you'll surely get from a capture with a directx encoder - or wrapper- like ATI and all his friends that work on the fly in software.
You end thinking that all in your system worked fine, but it's because there is a (holy) padding stream that helps your decoder to get through the mess he's reading.
I want to point that the final output from the encoding resembles more a transport stream than a system (-video-) stream and I've found that often also the best Mpeg editors usually go crazy when dealing with transport streams - probably because we are not able to instruct them as we should.
Btw M2-Edit is really a GREAT editor.
If this is the case, a useful tool for demuxing and repairing a "crippled" system stream (e.g a stream with lot of padding) is PVAstrumento from offeryn.com -freeware. Demux and remux, then join.
Womble - as pointed from Rich and other in this forum -seems to be capable to deal with padded streams(e.g. joining them with minimal loss of sync).
But I've never had consistent results.
But if your stream is a regular system stream then... please excuse my long post

Let me know
Brambus