I'll bet it's the kind of footage you're working with that's the problem:
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, 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.
Sr. Promotion Producer
KCRG-TV (ABC) Cedar Rapids, IA
The footage I am working with was shot on a 5D and I know that it shoots in H.264, but I have tracked to footage shot on the same camera using a different Mac Pro and it worked out fine. Also, the footage that is being tracked to in AE has been exported from FCP as ProRes 422, so I dont believe that the lack of information in some frames would still be an issue.
Maybe I am just experiencing a persisting hardware issue?