Not knowing whether you switched the IDE cable-ends at the drives or at the board, try fully switching the cables and see if your situation changes. If it does, you might have a bad cable. If it does not, the secondary controller may be bad or the BIOS may need to be reset.

I couldn't tell you what you'd specifically need to do for your given BIOS or motherboard, but look within the BIOS for a function to clear or reset the BIOS or NVRAM.

If you successfully clear the BIOS/NVRAM you will need to reset your clock and will need to do a redetect on the devices (they should be found at POST). If after this you still experience the same problem, you may have a bad secondary controller on that board.