The Animation codec makes huge files, so reading them from the disk can cause playback stutters on a slow computer (or a computer with a slow disk or slow connection to the disk).
Do the glitches persist even when you render and encode your final output out of FCP? If the glitches persist even in the final output—when you’ve encoded to your delivery format—then the problem is different from my guess.
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Todd Kopriva, Adobe Systems Incorporated
putting the ‘T’ back in ‘RTFM’ : After Effects Help on the Web
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