I downloaded the Quicktime update about 2 w...

I don't think this is related to your Quicktime upgrade. What you are describing sounds like a Finder crash and reboot. This would cause all Finder windows (folders, icons, etc.) to disappear from the screen, but would not affect any other open application such as Safari or Entourage.
In Applications/Utilities there is a tool called Console. Launch it. Click the icon "Show Log List." Click the flippy triangle next to ~/Library/Logs. Click the triangle for CrashReporter. Click on Finder.crash.log. Yeah, it's a lot of gobbledygook, but see if the crash times correlate with the times you saw your screen refresh.
The source of crashes like this could be a startup item (System Preferences / Accounts), a third-party System Preference, a corrupt preference file, or a dozen other things.
Create a new temporary user account. Log out and log in to that account. Work from it for a while. Do you still get the resets? If not, the problem is not in the OS, and is not a public System Preference. You may have to remove your startup items and deinstall any additional System Preferences you have added to see if the problem goes away; then install new versions of each of them until the problem comes back (if it ever does -- the problem might have been an old version).