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Go to device manager and uninstall the offending hardware. I had the same problem running Windows 2000 with dual DVD burners. They both stopped working and I tried unplugging them and rebooting-no luck. Tried fooling in the BIOS - no luck. Tried reinstalling the drivers - no luck.
The uninstall worked! After a reboot, Windows found the drives and installed them
You can run a disk manager for your drive however, I'll bet you will find its windows boot.ini. It may read just fine for a dual boot system but think about this. Windows can get confused real quick. I'm talking about the regestry. Take the time and do a fresh install of your Linuex and than re-install windows "clean install". I'll bet everything works out just fine. When 1 changes MB's there is a whole list of new drivers PCI devices loading into windows. Your system will run better with one copy of drivers for your new board and windows will not carry a list of old drivers and PCI devices of your old board.