I had the same problems. I use a program called "Sony Vegas Movie Studio" to make a Divx file of the Rifftrax and movie together. I had to stretch and move the last part of the Rifftrax a lot to get it synced up with the movie. So your not the only one that had problems with it. My big problem though was with the sound track of Casino Royal. It basically goes like this: whisper, whisper, whisper, BANG!, BANG!, BANG!, whisper, whisper, whisper.....
I spent a lot of time adjusting the volume levels of the movie and the Rifftrax.