Matching the GOPs lengths prevented the hitching between cuts, but occasionally I get a serious probelm.
Between the end of a re-coded clip (CCE) and a DVD Clip the video is rejected by DVDMaestro. That would be ok, there are alternatives, but watching the edit with media player causes a speed up right at the edit point. A DVD created within Womble freezes a standalone player.
I tried matching Field Top First (which I would think means nothing on progressive video), I tried fixing the GOP lengths, I tried closing all GOPs, nothing seems to prevent it.
Edit: Also tried encoding with the last frame forced to an I frame.