The movie and Rifftrax totally sync up till the end of the love scene at ends at about 54 minutes into the movie.
I just updated my copy of this to the anamorphic widescreen (I originally made it before I had a HDTV and didn't care about video), and I discovered that my old audio tracks didn't line up. I know I have the correct version now, but the old dvd that I used must've been the wrong one. There isn't much different in the tracks, though. The correct dvd audio starts about 2.524 seconds earlier, and there is about 1.1 seconds of extra audio at the 54:38 mark that throws off the end
. That's probably what you ran into.
I guess what I'm saying is...at least one other version will work with minor editing of the riff mp3.