Secondary drive failed, but now pc wont boot

[Clockwork_Killa]

One of my drives has failed, over the past few days it has gone from making odd clicking noises, to now refusing to spin up whatsoever. Im sending it off for RMA and I had the good sense to get everything I needed off it before it died.
The problem is that now I cant get windows to boot. I disconnected the drive, but it keeps trying to look for it in order to run a disk check. Is there any way I can stop it from doing this or is there another reason that could be causing windows not to boot when the disk is removed?
Thanks

Edit: In case it helps, its a wd raptor sata drive

[GoNz0]

try booting into safe mode ?

[clairedc]

Check the bios boot order?

[watercooled]

Maybe Windows put the bootloader on your second drive? Sounds like a stupid thing for an OS to do but it's happened to me. You could try booting from the Windows CD and run automated system recovery, that should make the system bootable again.