I was going to show the results of this Avisynth script to align the 2 scans. On double-checking before posting, I noticed the video of one film was shifted by 1 frame even though none of the settings had changed (and were printed onto the picture). Going back and running it again, they then were properly aligned, with the same settings . .
Clearly something in Avisynth (this system is running v.5.8) is wrong and cannot be relied upon to serve up the correct images.
I rather doubt it. It sounds more like a decoding problem. What are you using to decode these videos and what format are they in?
By 5.8, I assume you mean 2.5.8. Try upgrading to the latest version. I prefer to stick to the 32-bit non-MT version.