Your RAID controller is a Promise controller bud. These RAIDs are notorious for booting up slow. I know I have one.
Just checked out your manual online. Sadly, I can't see a way to disable your Promise controller. The only thing I can see is a ATA-100 / RAID jumper option on Page 2-3. By default its ATA-100. I see no option to disable it in the BIOS. Perhaps they added this option after the manual was published? Do you have any extra documentation specifically about the Promise Controller?
Regardless, RAID controllers are not good for anything but Hard Drives anyway. RAID manufacturers warn about this. The drive may well work on this controller, but I'll bet your Motherboard's performance is hindered by this setup.
Also, the DVD-Rom on this controller may be the reason for the long boot times...especially since its not designed for it. Disconnect it and see if it helps.