TMPGenc is'nt such a bad tool. It's just misunderstood and takes a lot of practice!
However, if you want to join a load of Mpeg's and turn them into DivX, Xvid or WMV9VCM files, why not have a go with MPEGmediator (v1.5).
It's a very small, easy to use program, which also has an Mpeg 1&2 encoder, (but it's not the best and I would not bother loading it).
I've never encountered any sync problems with it.
You could always turn your SVCD files into 'high bit' DivX etc files, using MPEGmediator and then turn them back into SVCD.