Non raid bios on ride chipset.

[Gravesent]

I have a 3112 raid sata controller, because the raid version isn't compatible with linux and unix I updated the controllers bios with the non ride versin, unix worked but I'm feeling a decrease of performance in windows, is it just me or is the nonraid version of the bios aplied on a raid chipset slowing me down.
Thank you for your time.