I noticed a similar (but different) behavior last evening...maybe related, maybe not, thought I'd add it here in case it helps anyone out....
I was watching a movie in Quicktime Player fullscreen with iTunes running in the background, along with other apps like Firefox also in background...
So every once in awhile Quicktime Player would go out of fullscreen mode ON IT'S OWN and I noticed the top menu bar and its text (at the very top of the screen that is...I'm on Mac OS X 10.5) would quickly dim, then go back to normal, as if Quicktime wasn't the active app for a second. Quicktime WOULD be the active app at the end of the menubar 'flash' though (unlike what seems like others experiences where iTunes would come to the front and stay as the frontmost app?)...
I was confused the first few times this happened as I'd never seen this before, and would just quickly Cmd-F to go back to fullscreen. Kept happening, though not at exact minute intervals, something close though but more random.
Went to iTunes and watched a video podcast fullscreen there....after a bit, same thing, it jumped out of fullscreen mode by itself. Very annoying.
Noticed I had set up a big queue of video podcasts to download, and switched to the download queue list...
It dawned on me that downloads were completing at somewhat the same intervals as my fullscreen video watching was being popped away from me! I tested by waiting until one download was just about to finish, then going to watch another video podcast in fullscreen...yep, it soon popped out of fullscreen as that download finished. Over and over...
It seems ridiculous that iTunes feels it needs to jump to the front for a split second and go out of fullscreen mode each time a download is finished, but that seems to be the case for me.
I haven't felt to the need to upgrade to the very latest iTunes (7.7 I believe, where they added the App Store for iPhone v2.0)....so maybe they could have fixed this recently?
Anyone else seen this behavior with the iTunes download queue? First time I'd noticed it, hadn't read about it anywhere before...
(apologies for the long-winded novella!)