I would guess your source footage is HDV. You will need to convert it to a different format. From Dave LaRonde at CreativeCOW.net:
If the footage you imported into AE is any kind of the following -- footage in an HDV acquisition codec, MPEG1, MPEG2, 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.
What source footages do you use? Per se there is nothing against of HDV/ DVC Pro/ AVCHD in Premiere and AE, but dependeing on what camera you have, you may be using one of the flavors that is not handled correctly by some Adobe apps. As Michael suggested, in that case conversion will be your only option.
I use a Full HD 1080i SONY Semi professional cam (2,930.00 $). I use AVCHD file format which is accepted by premiere and after effects. I could convert it but I would not like to spend time since this kind of format is accepted by the software.
I don't have these problems all the time. Eventually I managed to export the clip properly. I think it has to do with temporal memory. I don't know. I have to check all the memory data for best peformance and best rendering. I think I have already done this but I will dig a little deeper in this..