Thanks for the reply. TMPGenc MPEG Tools was the only one that'd touch it. Because it's HD video, most of the muxing programs die. Cutterman uses multiplex so I tried the standalone version. It did multiplex, but, the file size was twice as big as it should have been. ImagoMPEG-Muxer started and died after about .2 seconds. So, anyone looking to multiplex HD video, it looks like TMPGenc is probably the best bet. MPEG2VCR has issues with the 5.1 AC3 audio for me. I'm waiting for VideoReDo to add a multiplexing option. They said it's high priority and will probably be in the next release. I can't wait.
Incidentally, in case anyone's wondering what it is I'm actually doing, I record HD streams off my HD cable box through firewire. I take the transport stream and edit the commercials out using VideoReDo, saving them as elementary streams. If it's small enough to burn to a DVD as an mpeg file, I'll multiplex them and burn it. Otherwise I use rejig on the m2v file to shrink it a bit, then multiplex them and burn it. This allows me to keep high quality HD recordings of all my tv shows. I typically only get one episode to fit per disc, but, given the price of DVD-5 media these days, that doesn't bother me.