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?