Well, I just installed windows 7 to a 60gb Agility ssd. When I did that, I didn't format my HHD that had windows on it, instead, I just set the Agility to be the primary boot disk. That's when I started running into all sorts of problems. If you format both disks in the same screen and then install windows on the SSD, your problems should be done.
Side note, if you decide you want to use the AHCI mode, make sure you turn it on BEFORE you install windows or you have to have fun in registry.