There's no performance loss once the computer is up and running (RAID is a superset of AHCI). But the point of the RAID setting is to allow you to create bootable RAID volumes. So if the motherboard is set to RAID, during the boot cycle it will temporarily transfer control to the RAID BIOS which will look for bootable RAID volumes, and give you a few seconds to hit a hotkey to enter the RAID configuration menu. This can add anywhere from 3-15 seconds to the boot time in my experience.
If this is a single drive and you did not set up any RAID volumes before or while installing Windows, you can try switching it to AHCI mode to see if it'll boot. As stated above, RAID is a superset of AHCI. So if you're not using any RAID-specific functionality, the two modes should be indistinguishable to Windows. Even if it doesn't boot, a Windows Repair should be able to get it working under AHCI mode. But if you set up the drive as a RAID volume, then you're probably stuck with it, and would need to wipe and reinstall to correct it.