The most obvious thought is that you need to install the SATA drivers or set the SATA ports in the BIOS to IDE mode. I assume here that the two regular drives are IDE?
One of the drives is IDE and the other is SATA. I also swapped the SATA ports the SSD was using with the HD that was using SATA and it was recognized by Windows. I will try reinstalling the mobo drivers and see if that helps and double check the SATA settings in the BIOS