I don't believe it's possible to have a RAID array on a controller and boot from a single drive on the same controller. You'll either have to boot from the array or (like you've already done) move the boot drive to a different controller.
What I have found is that you must either be IDE or (AHCI and/or RAID). In other words, Zoron is exactly right! IDE and newer Intel setup configurations are not friendly with each other. My MoBo has the option of setting my interface to be Raid, AHCI, or IDE.
My system is all set up and I'm not f*ing with it, it works great and is faster than any embedded setup I've had in the past! When I am in the bios and I select 'raid' and only have a single drive, the later 'Matrix Raid' bios screen allows me to set up a single drive as a 'raid-ready' device. I can, in the future, add other drives and easily convert to to Raid 0 or 1 and if I add 2 drives I can convert to raid 5 (truly the list goes on)...
I am currently running 4 500G seagate drives set up (using the intel matrix bios) as a 400G raid 0 volume and as a bit more than a 1.25T raid 5 volume. I've never had a problem with it and I am a happy camper but ymmv.