Do you have a taskbar button for the updater? If so, what happens when you click on it a time or two? Does it disappear offscreen into the upper left corner by chance? I'm only mentioning this because I have been having this very same issue which affects any applications that normally run in a small window (eq2maps, spybot, adaware, etc. Even my windows task manager does this!!).
I had a friend that works in a computer repair shop take a look at mine, and he told me that it looks like I have a virus that has somehow manipulated my computer into thinking the center of the desktop is offscreen. You may be thinking to yourself "But I've already done virus scans, and none are found!!" I, too, have done the same thing with the same conclusion. But nowadays, virus programmers are good at making their 'works of art' undetectable by the more commonly used anti-virus programs out there.
I have yet to actually clear this up since I'm kinda short on cash and time (full-time student doesn't leave much of either in generous suuply
), but the quick (although temporary) fix I've found is to reset your resolution to 800x600 with all windows closed, then set it back to your desired resolution.