Sounds like the source (or at least some of it) was interlaced or telecined. Probably the latter. You'll need to IVTC the video source (dgindex->Gordian Knot AVISynth Script->TMPGEnc to a new M2V/MPV file, change the name of the original stream to .bak and then the new stream to the name of the old stream, and then re-open Womble and re-export the streams.

It sounds more involved than it is. The only command you'll need in your AVISynth script is the telecide command. Go with what Gordian Knot selects by default. Make sure any crop and resize lines are commented out.

I just had to do this with all the deleted scenes from Blade Runner. I was very surprised to see them telecined but they were. At least they were 16X9.