I have a setup with one SSD and one HDD, plus the latest Intel RST (Asus P5Q MB = P45/ICH10R). Everything is normal, however my SSD (which contains the OS) is not detected as a system disk. The HDD, which contains my old Windows 7 on a partition, is detected instead as the system disk.
Additional details: I have moved the pagefile and the TEMP folder away from the SSD to limit the writes on it. I guess Intel RST detects the OS disk based on the pagefile?
Also, my setup, if needed:
Windows 7 x64 Ultimate SP1, E7200, Asus P5Q, Kingston DDR2 800 4 GB, Asus EAH4850 512 MB, M-Audio Audiophile USB, Fujitsu-Siemens Amilo LSL 3230T 23", Corsair SSD x64/Samsung F3EG 1TB, Logitech Wave keyboard, Performance MX mouse
Look in Disk Management to see if it's detecting the SSD as the system and boot drive (it's under Administrative Tools on Control Panel). In Disk Management, the SSD should probably say System and Boot, and the mechanical drive should say Page File. There's some other stuff there too - crash dump, etc. - and they should both say Primary Partition.
I wonder if your BIOS is still configured to boot from the mechanical drive.