I would double check that the switches are registering the right switch numbers in switch test. It's possible that everything seems to be working and the switches are all giving numbers in the switch test, but they're the wrong numbers. In cases like this I'll use PinMAME to check what the switch numbers should be, then confirm in the game.

Also keep the cabinet switches in mind (connector J3). They share strobes with the playfield switches.

Could also be that the switched illumination voltage is shorted to the switch matrix. I would try it with F1 (switched illumination) pulled just to eliminate that as a possibility.