This is an old thread, but for others with the same boot drive troubles, it happened to me on a couple of iBooks, recently, and here are the reasons why the fault occurred:
1] Check that the ribbon cable to the drive has not become detached from it's socket on the other side of the mainboard. The connector is hidden under tape, and that tape can hide the fact that the cable is loose. The connector becomes undone very easily.
2] Check that you have actually connected the ribbon cable to the drive correctly. It's easy to connect only one row of the IDE connector pins, and that error is only seen from below the drive.
Hoping that this helps others.