Thanks. I think I had this problem with XP before, but IIRC it went away, either with unlocking the taskbar, changing the "stay on top" option, locking, then reversing the procedure. I can't remember.
However, this is x64 (which I would assume is heavily based on XP anyway).
It's just with some balloon tips, like my torrent client or FTP client, I use them for useful information to save me opening the program, and it's quite annoying.
Edit : I've just tried unticking "Keep taskbar ontop of other windows", and funnily enough, the popups now appear OVER the taskbar (which I require), but UNDER windows.....
Where's Bill went you want to give someone an angry slap?