I had similar issue.
I rebooted to BIOS, double-checked the drive order and disabled a couple things I don't use, like the floppy 3.5 drive socket and then went back to Windows.
Upon reboot, all my drives appeared in the drive listing with appropriate icons and labels.
But after going over it again, I think it just takes a double-reboot on Win 7 to get your hardware identified after you install it or change it around.
So you would install your drives how you want, boot to BIOS, make sure the boot order is set, then go to Windows and then restart again.
That's how I fixed mine.
Everything works fine now.
For some reason, Windows 7 is not refreshing for drive changes after the initial reboot - probably just a bug.