Found this at one point in time.
Warning: Numerous sites have hosted an incorrect pinout list for Burgertime.
Burgertime and Bump n' Jump (Both DECO, both licensed by Bally/Midway) used virtually the same connectors... all but one key piece.
This linked one has the correct information for Burgertime, but is wrong for Bump n' Jump.
36 Pin Connecter
Solder Side | Parts Side
--------------------------------|-----------------------------------
+ 12 V | A | 1 | + 12 V
----------------------------|---|---|-------------------------------
+ 5 V | B | 2 | + 5 V
----------------------------|---|---|-------------------------------
GND | C | 3 | - 5 V
----------------------------|---|---|-------------------------------
Pin 3 should be -5 on a BurgerTime. Pin 3 should be GND on Bump n' Jump. If a BNJ board is connected it will short your -5 to GND and either shut down or burn-out the power supply. I submitted a correction to Mike's Arcade which did update it on their site.
In any case, I don't know if this is in any way associated with your problems.
I haven't read the entire thread, but I'd consider checking a few things like how many amps are being pulled by each of the lines.. +12, +5, -5.. Connect just ONE of each of them to JUST the main board (remove the interconnect cables too) and run them through a DMM's amp reading . It could be something is shorted out and causing the switcher to go into shutdown mode. I would expect the amp draw to be < 1 Amp on the 12V and < 7 amp on the 5V for just the main board. Just a guess, I haven't metered mine.
If everything reads right, then start connecting the interconnects and the second board, all while still metering the amp draw of each line to make sure somethings not shorting or isn't overdrawing the max amps of the switcher.