I'm not surprised he's scratching his head, a main board change should have solved this.
I imagine this would also have changed the actual panel memory switches, since they are soldered on to the board?
But you have already discounted these by using the footswitch; an alternative method would have been using the panel memory increment in the control preset bank of the performance pads. But from your description this would not prove anything or help now.
I would try taking the ew65 out (and any other card) and doing the hard initialise, just to confirm that the problem remains.
Apart from that, the only other thing could be a subsiduary board, but I would expect all the software controlling panel memories to be located on the main board.
Most perplexing! Sorry to hear of your problems, Dave