Getting Weird Glitches After Rendering

I'm doing a big project with a lot of Motion files that we render in FCP. I had to have them as motion files versus QT because... long story, but after much trial and error it was the best solution.
Maybe a ten to twenty percent of the time, when I render these bits of the sequence, they get weird glitches. Sometimes lines across the non-alpha section of the motion file. Sometimes flashes of color across part of the video. When I simple copy the clip, delete the bad one, drop the copy in, and then rerender, it works fine. We were rendering to an external eSata drive. We're now rendering to an internal eSata drive-- just to see if that makes a difference.
Anybody ever seen this problem before?
Thank you,
Alex

NTSC, started as Digibeta. The Motion files however were created from image sequences that were starting as PAL. We converted them and have had good results, except for this 10-20% with glitches on rendering.
Thank you,
Alex

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