Not enough information to respond.
The lamp matrix in Star Trek LEs is a weird pre-node board type of arrangement. The CPU sends a signal to the "node boards" which then are turned on/off by the microcontroller on the board.
Based upon this; I'd look at the power supplies in the game. Namely the powersupply on the main node board controlling the center misson inserts.
The other thing to do is if he has any non-stock mods in the game. They need to be disconnected before continuing the troubleshooting.
The controlled Insert power supply basically comes from the main node board. Any GI and/or RGB inserts are driven from that PSU. It's super sensitive to any non-stock loads. There is actually a current sensing circuit in this PSU; if the load is sensed to high; it will "turn off" the LED powersupply temporarily which leads to "flickering" of all inserts and other weird behavior.