Try this: When you launch IE, and no window appears on the desktop, press Alt-Space. If the window menu appears, select Move, then press the arrow keys to see if you can move the IE window back into the viewable desktop area.
I have to do this frequently; I have a laptop, and when I’m at work, I have both the LCD and a CRT, with the desktop expanded across both screens. When I go home, some windows will try to display onto the non-conencted CRT secondary screen. I use the above method to drag the window back into view.
You likely don’t have multiple displays on your Win2k server, but the principle is the same; a window may try to draw itself outside the viewable area.