@acoustified: In After Effects, in the Project window, select the clip, right-click on it, select Interpret Footage>Main>Frame Rate>Assume this frame rate, and type in the correct fps.
Explanation: When you first install AE, it defaults to using 30fps for all imported image sequences. If you never changed that default (Edit>Preferences>Import>Sequence Footage), it will continue to do this. If most or all of your footage is a particular frame rate (like 29.97, 25, 23.976, etc.), then change it here. Otherwise you have to make sure to check and/or change the Frame Rate for each imported clip. Cheers!
...oh, and let me know if this helped, ok?