Hey, I've been having this problem ever since I got AAE. I have AAE CS6. Whenever I try to pre-render a video on AAE, it's fine, but if I save the project, open it again, then pre-render it to see the project, a black screen start flashing every 2 frames or so in every clip. I can't edit anything anymore. There was one time where I did that and it was fine, but that project was 11 seconds long. I'm not sure what's happening, is there any way to fix it?
What does "pre-render" mean? Are your force cacheing the comp to the disk cache? Actually render out a sequence/ clip? From your description it sounds liek you're merely doing RAM previews and the disk cacxhe flakes out. If so, try setting it to another location or turn it off completely in the prefs. Apparently your disks aren't up to the task and drop frames...
If Mylenium's suggestions don't work, then we need to know a lot more to help you. Please provide answers to the questions listed here: "FAQ: What information should I provide when asking a question on this forum?"