It is about the only encoder that works across Windows, Mac and Linux without running into missing or proprietary decoders.
I do have some video fragments at work that came straight from a Canon Powershot and Cinelerra has not problems keeping video and sound in sync. I'll see what encodings those use.
Would it be worth it to temporarily swap the DVD burner to the desktop machine (assuming you dont' have one SATA and one IDE box)?