AE Skipped footage + lost transitions

Hi everyone, in desperate need of help and your collective expertise.

I import a Premiere project into after effects CS3 to apply vfx, but Im getting some really frustrating errors.
1. For some reason, the additive, dip to white and dip to black transitions from my PP project will not work. They appear as a layer on the timeline, but where the cross dissolve will function fine, these transitions will not work.

2. Sections of my footage have moved. Straight after i import the PP project, i can scroll down the timeline of my composition and find sections where the layer of footage is of a different point in time than it is in PP. E.g Where an actor would be saying his line, he's now standing waiting to say it.

3. Whenever I first open a project after closing it, I am informed that my video files could not be found. I can double click on their pathway and locate them manually and its fine after that, but it happens once for every new project.

Im using CS3 across the board, Ive uninstalled all my plugins, could these problems be related?
Any suggestions about why this could be happening, how to fix it, or ways around it would be much appreciated. Its really getting me down and my deadline is starting to loom.

Cheers

David