I bet the these two facts -- 1) it's an H.264 file and 2) you run AE 8 -- are messing with the footage interpretation.
AE 10 has come to grips with long-gop footage, but you're on AE 8, so the following still applies:
Dave's Stock Answer #1:
If the footage you imported into AE is any kind of the following -- footage in an HDV acquisition codec, MPEG1, MPEG2, AVCHD, mp4, mts, m2t, H.261 or H.264 -- you need to convert it to a different codec.
These kinds of footage use temporal, or interframe compression. They have keyframes at regular intervals, containing complete frame information. However, the frames in between do NOT have complete information. Interframe codecs toss out duplicated information.
In order to maintain peak rendering efficiency, AE needs complete information for each and every frame. But because these kinds of footage contain only partial information, AE freaks out, resulting in a wide variety of problems.
I'm a Mac guy, so I like to convert to Quicktime movies in the Animation or PNG codecs; both are lossless. I'll use Apple's Compressor, Adobe Media Encoder or Quicktime Pro to do it.
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