The old version of the board DOES work, it just needs some tweaking.
All I did was snip off the pins of the connector on the board until they were about 2mm long, snip off the white "teeth" of the connector, and then solder the wires directly onto the pins (making sure I got the order right). This meant there was enough clearance for the board to sit behind the ColorDMD. I screwed it back on with short screws and it sits pretty flush to the speaker panel - in fact the LEDs are sitting inside the jackpot holes.