Ok mystery is half solved. I have 2 NeoGeo type controllers I wired up myself. First one is a DPD clicky PS3 game pad that I highjacked the buttons and just wired them directly to a NeoGeo DB9 extension cable. This has been working for all of the PCB and NeoGeo games I have. 2nd is an DIY arcade stick with Sanwa stick and buttons I wired the same way. For whatever reason, S16 works fine with the joystick, but when I press the start button on the DPD controller, it thinks every button's being pressed at the same time per the service menu controller test.I'll check from that angle, thank you!
I just wanted to report back that this isn't a multi issue to close this loop. Not that I ever thought this was an issue with the multi, I just didn't know enough about it. This is now an issue with my controller on System 16B.