We have similar issue:
Video was rendered using AE CS4 (v9.0.2) in QT (v7.6.2) at 23.976 fps.
When re-imported into AE, the footage was correctly interpreted as 23.976. However, when this clip was rendered out again (from 23.976 comp), the end result is such that there are 24 physical frames a second but many frames were skipped (by repetition). Therefore, you have a 23.976 fps video but with a motion effect of half that frame rate.
This can be solved by opening up the initially rendered file in QuickTime, and re-export using QuickTime. Only then if you re-import the footage into AE CS4 that the render will be correct.
Chit Yee
Spinn
Singapore