Strange Flicker

This is tricky to explain, but here goes:
My friend shot a movie on Super8 and had it transferred to video (sd, interlaced. 29.97). Whereever he spliced the actual film together, the film jumped so the video captured this and at every cut the film frame jumped halfway up the video frame, leaving a big white space. The jump usually took place over about 8 frames. I added letterboxing to the video to give us some room to play with and then went through the video and at every cut, I separated the frames and recomposed them to the best of my ability. Sometimes the jump was too big; it jumped more than the letterboxing allowed me to correct, but mostly I got the video looking pretty good. Of course, it still shuddered and jumped somewhat the way most super 8 films do.
So the director was quite happy with it. But when I export the film, either to make a dvd or exporting to quicktime uncompressed, or when compressing, some of the cuts really flickered. This doesn't happen when I watch it in fcp. Whatever variables I tried playing with--key frames, frame reorder, deinterlacing--these ugly flickers remained. I decided to uploaded a small clip so that I could ask about it here. However, once the clip is uploaded to youtube it no longer flickers. Yes, as you'll see it shudders and jumps, but this was one of the worst parts of the video and the way it looks on youtube is actually a huge improvement over the original. But my question is, How is Youtube fixing the flickering? And how can I fix it with fcp. What we really need to do is get the video onto a dvd for festivals.
The clip is below.
Thanks for bearing with the long explanation. Any help is appreciated.
Swink
http://www.youtube.com/watch?v=q0RLif90rPs

The thinking at the moment is to send a dvd to a few festivals the director is hopeful about and then do another telecine. So we want to send something that looks the best it can, relatively speaking.

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