The audio track is off a tad on my XVID of Ghosthouse (not the rifftrax but the entire audio track including the rifftrax). Here's how i fixed it:
download Virtualdub.
File...Open Video File...Open Ghosthouse Xvid
Audio...Interleaving...Delay audio track by -200ms...ok
Audio...Direct Stream Copy
Video...Direct Stream Copy
File...Save as AVI...ok
tutorial: http://www.tutorialsroom.com/tutorials/av/vdub_adjust_sync.html