I've been scouring the forums looking for someone with a similar error to mine, but I haven't had luck. I'm going to keep looking after I post as well, just in case there was an oversight on my end.
I've recently rebuilt a system from the ground up and currently running Vista 64bit. I reinstalled all of my old software and put it on here, and that's when I noticed weird sorts of nuances that have happened.
I typically do video builds in Premiere Pro CS3 and then import that project into AE CS3 for the final touch ups. What seems to be happening, is that when I pull the project into AE, rather than having my footage be footage, it precomps the footage. So all of my clips start at the beginning of the clip timeline. This is especially apparent and frustrating when I get one avi clip from a client with all of their selects. I import that, there's the video clip but also the precomp and all of the footage in the main timeline is referencing that precomp.
I don't nest the footage within Premiere. I've even gone as far as re-exporting out a movie of the footage just to see if that fixes it. I'm out of ideas at this point and I can't seem to find anything within the import options to say "for the love of God, please don't import footage as precomps".