Doctor M said:ADM's video is a mix of 29.97i and 23.976p video. So short of re-encoding to full progressive, this needs to be edited with the pulldown flags intact(?)

It does. Have you tried re-encoding the whole audio? I can't think of anything else. It's been years since I used Womble.

Does the end product have to be a DVD? If not, you could perform an inverse telecine, edit in another program, and use then x264 to recompress. With decent settings, you probably wouldn't notice any difference in quality.