Premiere Pro import issue with transitions

When I import my project from premiere, none of my transitions except for crossfades will work.

Even though CS3 transitions are supposed to be compatible, this would be work aroundable, because transitions have been replaced with a solid that marks its place, and i could just use AE's transitions but some of my footage has been re-aligned.

But my project window informs me that about half of my video files are "missing", but and when i scrub through the footage, the video layers are there, but the layers are from a different section of footage. Relocating the files does not fix the problem, the video is still of the wrong section. Premiere doesnt pick this problem up, it shows all the footage in the timeline in the correct place.

I could readjust all the footage and get the correct sequence back, but the real problem is that the crossfades have embedded themselves in the footage, so when the shot is wrong, I get a crossfade halfway through the footage i need.

Ive reinstalled and all that, but Im sure theres a solution out there, Im completely out of ideas and will listen to anything.

Dave