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Where and how are you storing your stuff? Everything needs to be in the same relative location (i.e. parent folder) for this to work properly, meaning your AE projects and the PPro project need to be in the same place and have the same access to the footage. Other than that this could be specific issues with teh source format and/or the media cache but based on your sparse info that's impossible to tell...
Ahh, that makes sense. My AE and AP project files are in the same directory, but not my media files. I'll try moving those and see if that fixes it.
Ok I moved all my media files to my main project directory. In Premiere, I selected a clip in my timeline and chose "Replace with AE Composition"
After Effects started up, created a new project file and composition but the media file still didn't show up in the project window. Is it supposed to? Or do I manually have to re-import each movie file into After Effects? As I mentioned, it seems like it will be a tedious task to import the movie files into AE and find that 3-second section again that I cut in Premiere.
Any other ideas or ways I should go about this?