Depending on your motherboard, you can go into the bios and change the boot setup. In there you should be able to find which devices are bootable. 1st device is usually A:, 2nd device is usually a CD-Rom, and 3rd is usually the Hard Drive. Here you would change the main boot device as the ATA device or which ever one of the hard drives it can see as bootable.
For me I take out all the unnecessary boot devices and go straight to my hard drive as the first one.
But I do warn you about changing anything in the bios... It's not recommended to change anything in it unless you are aware about what you are doing in there... It's like messing with someones' brain.. Good with the right tweaks.. Bad with the wrong tweaks.. And if you ever do mess up the bios, read the motherboard manual about how to flash the bios to restore it to manufacturer defaults.
Anime2Envy is also right about Raid..
But you will also run into the same problem if the onboard raid or raid card craps out...
