Have SATA Raid on standard spin drives. Have slave ide spin drive. I upgraded today to a singe Crucial M4SSD 64GB SATA drive. It has win7 installed and updated. I am currently typing this while booted on this drive. All drives are accessable through windows. BTW, this is on a Asus P5ND Mobo.
Ok, this is where it gets wierd.
In bios boot options I have it set to boot off of the CD-Rom with the Win disk in. Then boot on HD's. The HD order for boot is SSD, Raid, Slave. While booting it says which OS do you want to load. Win7 or Win7 (ssd or raid). I select SSD Win7 and it loads fine.
If I set it to boot off the HD and not off the CD... I get a replace system disc error.
You can edit those using msconfig and selecting the Boot tab. You likely had an old OS install on one of your other drives which Windows saw and left a boot option to it. You can delete it from that menu.