The MPU board 6821 PIA chips can be determined as "faulty" during the power on self test if one of their port A pins are shorted to ground or something else.
U10 port A controls the switch matrix, lamp board and display numbers.
U11 port A controls the display digits.
All the lamp and display signals go through MPU J1.

If by chance when you were diagnosing your 12 volt issue did you disconnect J4 from the lamp driver board and accidentally reinstall it off by one pin or upside down?

The only way I can see J1 and/or J3 from the lamp driver board to cause this issue is if there's a shorted lamp socket to a switch on the playfield - but even that's a bit dubious.

Don't reterminate your connectors for this issue. The error condition was a short circuit, not open circuit.

Which one is it? J1 or J3?

Does disconnecting J2 and J3 (playfield and cabinet switch matrix harness respectively) from the MPU board make any difference?

Do you have the earth braid at the base of the head connected to the cabinet earth?

What happens when:

(a) When the lamp driver board is not screwed down, are all feature lamps on the playfield working properly?

(b) Everything is connected but you don't screw the lamp board, how much voltage do you measure between the grounded metal shield in the head and the GND test point on the lamp driver board?

(c) At the lamp driver board with J1 and J3 connected and screwed down but disconnect J4 from the lamp board?

(d) All four connectors are connected to the lamp board and screwed down but you disconnect all other playfield connectors (i.e. MPU-J2, SDB-J1, SDB-J5, Rectifier board-J1)

(e) All 5 displays are disconnected

Ok, two more if you don't mind. What happens when:

(f) Everything's connected and screwed down, but disconnect J2 from the lamp driver board (LDB)

(g) Everything's connected and screwed down, but disconnect J4 from the solenoid driver board (SDB)

Can you retry (b) from above but take measurement in both AC and DC voltage?

If possible please post a clear picture of the J1 connector at the MPU board clearly showing all wire colors and same with J4 at the lamp driver board.

That second picture showing J4 on the lamp driver board, you can see nine red resistors on the board.
With the machine OFF, and your multi-meter set on resistance mode, black meter lead connected to ground, how much resistance do you measure with the red meter lead on the left side leg of each of those nine resistors?

Readings are good.

Can you please clarify this, are you counting the initial power on flicker as a flash?

Can you post a clear picture of the J1 connector at the MPU board showing the wire colors, and also a general picture of the MPU board.

Since this started at the time you repaired the rectifier board, what else did you touch at that time?

Long shot, is there something behind the lamp driver board that's shorting?

If you put the Mata Hari MPU board in this game and disconnect J4 from the solenoid driver board so wrong solenoids don't activate/lock on, what happens?