Unplug the 8-Driver PCB in the backbox. (Connected by the small ribbon cable.)

See if that changes anything.

Okay - then:
(1) Likely, your ribbon cable is flipped. Check, Double-Check, and Triple-Check that when you plug the ribbon cable back in, that the RED LINE on the cable goes towards the "1" pin on the CPU and the "1" pin on the Driver board.
(2) If you are very, very, *very* sure that they are, and you still have the problem, reverse one of the plugs.
(3) If there's no change, you will need a new 8-driver PCB.

Sure -
That's because the 9th column (which is for the Clock Optos) is driven by one of the outputs on that board. By plugging the ribbon cable in backwards, the signals getting to the board are corrupted, and causing that column driver transistor to always be on, which would then cause the 9th column to always be grounded. When an opto on that column was NOT blocked, that ground would then be read by all the other rows, scanning all the switches, and cause it to report that.

Yup! Since an opto board connects to a specific number of columns, and all rows, a bad driver or blown board can cause the same thing.

The key was he stated some flashers were stuck on as well - like the column driver, other transistors drivign the flashers would be stuck on, causing them to always light up.