Odd Rendering/Export Issue

I have had a weird glitch lately, when I export a Self Contained Quicktime Movie off of certain timelines the Quicktime File will have randomly placed frames quickly garble onto the screen totally out of place. Like a frame will show up on a clip, from a clip that played before or after it. This footage is HDV 60 1080i. One thing I have discovered is if the clip has any sort of Filter on it, it will be fine! So if I just place a clip on the timeline and export it will have the flaw, but if it has a filter on it it works great. With me almost, if not every shot has a filter, so this is something that I just noticed when exporting raw footage for review.
Any clue why straight footage on a timeline would have an issue, yet filtered footage is fine?
I'm on FCP 6.0.3 with OS 10.4.11 on a 2.66 Quad Mac Pro.

Is it possible that the footage that is unfiltered is relying on RT effects to play, and would need to be processed if you were going to tape with it? Try processing all the RT footage on the timeline.
Are you re-compressing all frames on export? Have you tried exporting with QuickTime Conversion instead? That usually looks much better to me quality wise.

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