This seems like a popular question lately, here is a likely culprit:

In Compressor 2.0, all Apple’s supplied presets seem to have Field Dominance set to "Top First" (aka "Upper Field First"), as you can see here. I went through a few and they were all set this way.

Since DV camcorders capture video lower field first, FCP capture presets and sequence presets are lower field first, as they should be, so interlaced fields proceed in order. However, when encoding video with Compressor, the field order is reversed, leading to very unpleasant, …