After changing over the LEDs initially, there was no problem until the next day. I would tackle this by ;

1 - Installing a standard display and check. I would expect it to work.
2 - Remove the factory plug for J116, and connect the ColorDMD directly to J116
3 - Remove only the LED flashers, or disable them by removing the corresponding connectors temporarily.

I'm thinking that one of the LED flashers is dragging down the +12V for the ColorDMD.

I've seen strange issues on older games with some 906 and 89 flashers on the market.