I see you recently upgraded the software chips. Did you upgrade the chip on the DMD too? Apparently, if you upgrade the MPU chips but not the DMD chip then the DMD might not work.
The two computers communicate via a ribbon cable. When the main CPU board needs an animation, it does a "call command" to the DMD CPU, which does the animation. You can sometimes see this on games that have mis-matched ROM software. For example if the main CPU is running ROM version 2.x and the DMD CPU is running ROM version 1.x, sometimes the DMD will show "Command 24" on the screen instead of the actually animation. This happens because the animation call number does not exist in the older DMD ROM version. For this reason the main CPU and the DMD CPU should both have matching version numbers (say 2.x for both the CPU and the DMD ROMs). In fact if the ROM versions are mis-matches, some pretty wacky score display screen behavior can be seen.
In addition to the communications between the main CPU and the DMD CPU via the ribbon cable, the PIA 9b on the main CPU board can cause problems too. This PIA (peripheral interface adapter), if damaged, can cause bad "calls" to the DMD computer. This can also show wacky DMD screen behavior and strange "command call" errors (like "command 9c") on the score display.
But this sounds more like your problem here;
Dot Matrix Display works for 5 minutes than goes blank.
This is a very common problem with all DataEast dot matrix displays, and is often related to the connector bring power to the display's computer board (mounted on the back dot matrix panel), or power to the display itself. On the large sized DMDs especially, the 5 volt .156" Molex connector going to the DMD's computer often needs new Trifurcon pins crimped into place (red and black wires usually). Also the 5/12/HV power going from the power supply to the display itself often develops bad .156" connectors pins too (on the display and/or the power supply), requiring new terminal pins.