Try:
With only the affected window open (and the taskbar NOT set to autohide)
grab the top of the taskbar and pull it up to twice its normal height. Then
close the window, resize the taskbar, reopen the window.
Or
With only that window open, right click the taskbar and choose "tile
vertically" (horizontally should also work.)
Or (a registry edit)
Q194759 - New Internet Explorer Window Opens Partially Off the Screen: http://support.microsoft.com/support/kb/articles/q194/7/59.asp