That's almost certainly because you have a video that contains 29.97 unique images per second, and you're telling AE to make it 23.976fps. It can do this in three ways: by discarding frames, by blending fields/frames together, or by slowing the clip down. So far, it seems that you haven't found a way of making it do the last of these.

But none of that really matters because you have a way to slow the video back down to 23.976fps. If Puggo really wants the video to be at 29.97fps (and I don't see why he would), you can do your work in AE, render the result, and then speed the clips back up with AviSynth.

AviSource()

AssumeFPS(30000,1001)

EDIT: Harmy, I typed all this before I saw the correction to your post above. I don't know why you are seeing combing with your project set to 29.97fps, but the fact that the DV codec is involved might have something to do with it. AE might be programmed to handle DV footage in a certain way.