It would be extremely helpful if you could post a couple screencaps of these "suspect" frames that you have mentioned.
Depending on how you deinterlace, it could throw off the timing.
Inverse telecine changes the framerate of the video, and is pretty much impossible to do to a finished AMV. If you are editing from avs scripts, and add in IVTC functions, everything will be way off, if it even works at all.
Decide on a method before editing. or edit interlaced @ 29.97 fps, then do some sort of deinterlace that doesn't change the frame rate to the finished video..
interlaced or progressive
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