well, According to Mikesarcade.com, Theirs only 1 mortal kombat jamma pinout for their lack of including an alternate one.
Ive used this site for a long time in building adapters for non jamma games and in every case ive had no matter the game, they are spot on.
so what i get is that your MK needs -5v to function.
I dont know for sure cause ive never looked into multi adapters
but my guess is that if you only have -5v on all the time, the board could not function and your board in the multi adapter that has all signals on would be dominant.
other thing is this.
many multi jamma boards ive read about supply power to both pcbs all of the time, and only switch video, sound, and controls.
in that case you should be ok to hook up a -5v wire from the PS to the MK Board without a problem, and it should light up.
Id like for anyone who actually know though to contribute before you try it.