I noticed that when I leave the game on for several hours, at some point, some of the switches become flaky. Most noticeable are the crate, the opto in the Bony Beast ramp and the start button. If I enter switch test, it takes 4 button presses to register one. Those switches are not on the same row/column.
At first, I could leave the game off for some time to fix the problem. But this morning when I wanted to retest, the start button was flaky from the beginning. I also notice that during switch test, the crate does not register anything when I tap it. During gameplay, it does register.
I tried re-seating all connectors related to switches, as well as the flat cable between the CPU and the driver board, to no avail.