Footage delivered to me as h.264 quicktime 29.97 fps shows a duration of 91 frames in Quicktime Pro. Same in After Effects CS6. In After Effects CS5 however, it shows a duration of 107 frames. When I step through the footage frame by frame, there are in fact 107 distinct frames. It seems to me the shot is much too short for so large a discrepancy to be caused by a drop/non-drop issue and too small to be a 3:2 pulldown issue. Any thoughts? I ask because I initially did my version of the shot in CS5, but I'd like to do some revisions in CS6 to take advantage of the superior caching performance. Of course my comps are all out of whack in CS6. Incidentally, another shot in the same sequence is similarly strange - frame counts match in QT Pro and CS6, but is longer in CS5 (strangely by a different ratio). Huh.
I've seen this issue before without many options to fix it. You can bring it into CS5 and export an image sequence. Then you can "replace footage" in CS6. H.264 is a complex format. It is always better to convert to other more "work-friendly" formats for post-production. MPEG Streamclip is a good converter.