Updated about 6 yrs, 11 mths ago (November 18, 2013). Know a better answer? Let me know!
How to fix when the Windows Taskbar refuses to auto-hide
Quite commonly (at least for me), the taskbar (which I have set to auto-hide) will refuse to hide, and sits on top of other things and gets in the way.
Killing Explorer will probably fix this (though it will also close any open Explorer windows you have open (i.e. folders). If not, check that the auto-hide feature is still turned on (right click the taskbar, check that “Auto-hide the taskbar” is enabled), and that an app isn’t constantly requesting your attention (usually by flashing itself in the taskbar).
To kill Explorer
Go to Start, Run (or Windows Key + R) and type:
Explorer will probably automatically restart. If it doesn’t, go to Run again, and type: