That makes me think you have a switch strobe (output) either shorted to ground or stuck low (bad IC).

Check start button blades and coin switches (especially the coin lock out wiskers).

If you have done the slam switch mod on the MPU, You can start a game and then unplug the edge connector that goes to the cabinet switches and see if the playfield behaves normally.

It means that the "strobe" they all share in common is stuck low. Could be a ground short or a bad Output IC.

Similar discussion here including snippet of the SW matrix showing the 7404 strobe drives.

https://pinside.com/pinball/forum/topic/system-1-driver-board

But if they all share the same switch return line, then it may be a bad 7405 or associated components.

Again, if you haven't done the slam switch mod jumper, you can jumper a cap on the MPU board with an alligator clip jumper. This way, you can unplug both the playfield matrix (J7) and the lower cabinet matrix (J6) to see if the issue is coming from wiring.

Glad you got it working without having to pay for a new MPU board. Switch matrix is one of the most common "damage" areas of both Gottlieb System 1 and System 80 due to the fact that the playfield has higher voltages present than the ICs can handle and when people get their hands in there and start fooling around with the power on (not saying you did!), its very easy to zap something.

Clay has a good write up on the slam circuit and mod. But personally, I don't like to permanently defeat the slam circuit on my games as its nice to have the slam switch present to exit out of test or restart a game without having to cycle power. But it is always good to know the location of that cap (missing in his photo) so you can install an alligator clip jumper for troubleshooting purposes.

http://www.pinrepair.com/sys1/#slam