Suztera :
The brand of the gpu doesn't matter. If you got an OEM window licence, you most likely have to get a new licence then. You could try asking microsoft if you can move it to your new motherboard.
I've never had a problem transfering my OEM licences. I just had to call them up when I upgrade. It is a problem if it was a prebuilt PC, but not if you bought the OEM Windows software with the disks and everything.