Windows can be picky like that. Actually may not even be windows\' fault, may be a number of other things. My PC has problems booting up if my mouse is plugged in the USB port, and it crashed WinME all the time (Win2K seemed ok). So I just keep it in the PS2 port for now.
You can try going through and seeing if there\'s a resource conflict...but if it works fine in the PS2 port, I\'d just leave it there.