OS is irrelevant for hard drive jumper settings. That is all controlled at the motherboard's BIOS level. You most likely need to set the jumpers on the hard drives appropriately. I usually just try to have everything on cable select and plug the drives in to the correct slot on the data cables.
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Creator of the Star Trek Mod - AST Mod - 78 Ship Sets - Conquest Mod - Atrocities Star Wars Mod - Galaxy Reborn Mod - and Subterfuge Mod.