First, update the code. There were definitely bugs in WPT. You don't need to update the ROM chip; you just need to update, which takes a USB stick. The ROM file should be on Stern's web site.
Second, Stern had a service bulletin out for WPT. You might see if this is relevant, but I don't think so. WPT was known to have spontaneous resets, but that's not the problem that you're describing. Anyway, Stern was replacing computers with a fix, and you might want to have that done if it wasn't. (This is a long shot but can't hurt... if Stern is still doing it gratis.)
But if that doesn't fix it, I suggest another look at the switch tests. I'm guessing here, but... I'm sure all the switches register, but I think your game has an additional problem. It sounds like a short somewhere in the switch matrix, causing spurious closures in one of the left or right ramp switches. That, I would expect, to advance through the cities and into WPT champ multiball. Is that what's happening? This can be a real pain to find, because the problem will not be with the ramp switches. It will be with switches that share the same row or column, but not those.
But update the ROMs first. You might even get better diagnostics that way.