The border of my windows disappears for a second when I'm installing something then closes and opens up another window continuing the install. I never had this problem with build 6801 32 bit. I'm now using build 7000 64 bit. I've been looking all over and haven't found a solution.
I had this happen to me, but it was when I was running a full-screen application -- I would minimize and open the browser, and viola! No border. This has only happened to me once though. I restarted the system and it went away
You could also try restarting the Explorer process, instead of the whole system.