Incredibly I just noticed that I failed to mention the possibility of progressive video with phase shifts and or swapped fields (fields in a reversed order).
This type of video is simply progressive where the field order is off by one field. Fixing it restores the image to progressive.
Will definitely have to mention it when I figure out what to do about the subtitles.
Has anyone played with BDSup2Sub yet? I'm curious what results people are finding.