It does not make sense that the SATA II ports are scanned first, and not the SATA III ports, unless you are using the "wrong" SATA III ports.
Your board has the main Intel SATA controller, and the add on ASMedia SATA controller. With the board mounted in a case, the two gray ports at the top are the ASMedia SATA III ports. The two gray ports below them, next to the black SATA II ports, are the Intel SATA III ports. The Intel SATA III ports will provide much better performance than the ASMedia SATA III ports. The Intel SATA ports are scanned before the ASMedia ports, which would explain why the SATA II ports are scanned before your SSD, if it is connected to the ASMedia ports.
Since you don't use the RAID 5 volumes in Windows, try this. Start disk management in Windows, and disable those RAID volumes. That should not affect them in Gentoo.