yeah ok, then that's not it. you verified voltage at the power supply, but did you do it at the JAMMA edge, or more importantly, a rom socket? just wanna rule out if you have significant power loss at all. Williams/Midway made their power wiring runs extremely long, it's not uncommon to lose like .15-.25 or in the very worse cases half a volt.
make sure your JAMMA edge connector's clean too. I never bothered checking this until this year, and boy what a difference it makes. just use a pencil eraser on the contacts if they're dark in appearance.. make sure the eraser shavings are pushed off the board though.
to test voltage at a rom, look for the U-shaped notch on the socket (they face upward) and stick one meter probe in the lower right hole, and the upper left. this is what your like pure voltage is, cause that's your component voltage. as mentioned, you can lose a lot of voltage between the power supply and a rom, in some cases where it's too low to operate the board.
another thing, I never tried this, are all your security chips installed? they're about 7 or 8 little chips above the game rom banks, and a big one in the corner by the U99.