Not a 'Big' deal, but it's Definitly noticable while watching the converted DVD.
Only thing I know to do is to 'splice' into the captured movie and take out a 1-2 second piece of the movie to account for the 'shortness' of the Rifftrax mp3, or splice into the MP3 Rifftrax itself, and stretch it out to the proper extension which would be quicker and easier.
But All the rest Lined Up and Converted Perfectly with No Modifications needed.