What is your workflow to get these AE files into PrPro? Did they originate in PrPro and were then DL'ed to AE for DL'ing back to PrPro? The exact steps might yield a clue as to what/why this is happening.
I import several files straight into after effects for editing (multi tga, jpeg, psd, etc), then import the AE file straight in PrPro for ading text and organizing. To work around the problem I had to put each AE file into different folders to keep PrPrp from mixing them up. Never had this problem with CS3, but doesnt sound like anyone else is experiencing this, which leads me to believe its something with my computer, I dont know.
I am running windows XP and have a second operating system (also windows XP) installed. Had to work around a virus that took over my computer. Could this be a contributing factor I wonder? Would delete the 2nd operating system but it wont, so cant test that theory.