RAID Controller Issue

Hello
So Currently Im using just a Simple Shuttle Barebones SS31T Mobo and there are 2 SATA ports on board, I have the port closest to the CPU plugged into my SATA HD, everything works and has always worked with no troubles, As of recent I'm trying to flash a SATA Drive from USB on boot but It will not detect the SATA drive from what I belive to be Non Installed RAID Driver, When I try to install the drivers from the main disc it tells me it is unable to Find RAID controllers and thats it, So how exactly do I go about getting thos correct drivers installed?