I take it that all the drive jumpers were accounted for?

The easiest way to check where the jumper has come from would be to check manually, starting at JP1 and working through them all in order until you notice a jumper missing then close the jumper (connect pins 2 and 3) with the cap. Reboot machine and see if she works...if not remove the jumper and carry on up the chain. Takes a while tho...

Or you could contact the mobo makers and ask them about it......