I've got a weird but annoying problem with Ae that started when I upgraded from Windows Xp to Windows Xp64.
"Live" parts of Ae (render view, timeline, etc) can be seen through any window that is in front of Ae. So when I'm using Firefox to browse the net Ae elements are seen over the web pages, making them impossible to read.
The only workaround is to minimize Ae whenever I'm doing something else.
Not sure if it's related, but Ps also has similar behaviour (the program beneath Ps will display for a moment during zooming). Ae and Ps seem to conflict with regards to GPU use, both want to use but only one can?
I'm not sure whether it's a Xp64, Ae or Nvidia problem, but's it's driving me insane! The problem occurs in Ae CS3 and CS4.
I've got the latest display drivers. I also get sporadic BSODs that can be attributed to my display drivers. So concentrating on drivers is probably my best bet?
I would advise against using Windows XP 64bit. It was never really fully developed, and you are lucky those are the only problems you have been experiencing. You would be much better off with Vista 64 or Windows 7 for a 64 bit OS.