ok, so this is what I did. First I unplugged all of the drives including the dvd drive, powered on, and got the 'insert media into selected boot device' message as I would expect.
Next I plugged in just the ubuntu drive and powered on. This time I got the same 'insert media...' message which I think means it doesn't recognize this drive as a bootable drive. When I checked the BIOS, the drive was recognized in the drive list though.
Next I plugged in just the Windows drive and powered on again. This time I got no message, it just kept trying to boot and then restarting. Again, the BIOS recognized the drive, but just won't boot from it.
Before these problems, I would get the normal dual-boot screen asking me which OS I wanted to boot and I could successfully boot into Windows and ubuntu.
My system specs are this:
CPU: Intel i5 Core with stock hsf
MOBO: Asus p7p55d-e pro
RAM: G.Skill Ripclaws, 2x2GB
HDD1 (windows drive): WD 64GB SSD SiliconEdge Blue
HDD2 (ubuntu drive): an old Samsung drive I pulled out of a busted Dell - 75GB
HDD3 (storage drive): WD 640GB Caviar Black
GPU: GeForce 9500 GT
PSU: Antec Earthwatts 650w
I don't have onboard video