Does win7 act raid controller without being asked?

Hello. I'm experiencing a rather unexpected behavour in windows 7!
Let's start from the beginning.
I've had issue with the JRAID controller encountering timeouts whilst using the system disk in windows 7 for 2 weeks or so. It got more and more frequent, and I can hear one of the harddrives in my system spinning up when it shouldn't be asleep in the first place. Given it only seems to happen when the system drive's in use, I'm assuming one of the drives is bad. I ordered a brand spanking new 2TB drive to compliment the other 2TB drive and the 7 500GB drives. Two of these are set up in raid 0 as system drive on the onboard jmicron controller.
After ghosting 660GB system over to the 2TB drive I went into the bios and set the jmicron controller to ahci mode (so the raid couldn't possibly be used for booting). Rebooted, and set the bios to always boot from the 2TB drive as first option.

Works fine. But for some rather odd reason I still see the old system drive, and files on it are still intact? I know the controller's set to ahci, cause red text warned me that it wasn't running in raid mode, but raid structure was found on the drives. Does windows 7 work as a software controller when it finds raid structure?
At first I thought it was just 'luck' that the partitioning table was intact on one of the drives, but I don't see the two individual drives in disk management - only the raid drive - as if it ran in raid mode. I did not expect that.

I'll try rebooting and setting the controller to legacy mode, but it's really wierd to see the raid set intact when I meant to break it!

for system specs see my profile.