all mobos have that connector, there's a sub-board that plugs in under the PCB and has a cable that routes to a JAMMA to mahjong converter. for the mahjong games
if that sub-board is connected, even if the Mahjong adapter isn't plugged in then non-mahjong games wont boot.
there are some other mobo differences though, I have a desert war cart that will boot on some mobos but not others, for seemingly no reason. Similarly I've got a boxing "cart" that only boots on 1 of the 5 JMS32 mobos I own... I really can't discern any significant differences between these mobos either. they all appear identical.
That was me. Interestingly my chips were labeled as 100ns and didn't work, and some of the factory chips are 120ns.. and did work but it turned out that my chips were ACTUALLY 150ns and had been painted over and re-labeled as a faster speed... So yeah don't trust the labeling on your EPROMs if they've not bare smooth ceramic. if the texture on the top of the chip doesn't match the belly of the chip they've been re-painted.
In my experience there is no difference in the Jumpers with any game on this hardware.
it's super annoying isn't it

one connector has 3 rows of pins instead of 2, that's how I visually orient it with the PCB case off.
What is the security chip number on your PCB?
Also can you show us which file you're installing on which chip and where? I can probably give you some guidance if I know these details.
EDIT: looking at MAME source it appears the "tp2m32" DOES have correctly named ROMs where the file extension matches the [##] location on the ROM board. HOWEVER I'd ask how recent your MAME ROM set is because if this wasn't always the case and you're using an older set with mis-labled ROMs that could be the root problem here.