TRy and turn of the disk caches completely. I suspect you are seeing a timeout issue with your RAID drives where AE somehow fails to update the cache databases....
Thanks for the input Mylenium, (I wish I knew your name. It feels kind of odd referring to you by you username)
I unchecked cache and restarted the computer to give it its best chance of making a difference, but no change. The Project and Exports drives are set to never sleep, so I guess it was a long shot. I have also made a close study of running processes during various states regards AE. The nearest thing to an anomaly I can see is that 'Adobe QT32 Server.exe *32' starts when AE opens, and closes when I exit AE. It does not reopen in the Task manager when attempting to restart AE. Just another occurrence of AfterFX.exe Further occurrences of AfterFX.exe appear with each attempt to restart AE
OK I just had an idea. I opened AE with a new Comp. Saved and exited, and AE disappeared from the Task Manager, and I was able to restart AE. So I'm thinking it is to do with file locations from other Comp. However, when I closed my Test Comp again, AE did not close out of the Task Manager, and I could not restart it.
I can see that it releases most of the memory after exiting. 500Mb reduces to 200Mb. The next occurrence takes another 40Mb RAM. Each attempt to reopen AE takes another 40Mb. I'm stumped. It's not life and death, and is not a huge inconvenience, but it would be nice to fix it.
If Quicktime is involved, it could indeed be a CoDec issue but those are usually a pain in the rear to unriddle. If you use DSLR footage, you might want to check it in Bridge for metadata. The same would be true for RAW files. AE is hyper-sensitive to that stuff. beyond that you would have to use tools like Sysinternals' System Monitor to have a look at the processes and file I/O and see where it makes a burp...