Did you test the connections to the buttons with a multi-meter?
Try just shorting them out by hand to see if it registers that way?
Unplug those buttons & swap them with a couple of the 1s that do work...(Conversely you can plug some wires for a working switch to them & see if they work that way)
Usually something like this comes down to a wiring issue-mostly a lose ground somewhere(especially when things have been moved around). If not, I'm not sure what else it could be other than a hardware issue.
Other than that, maybe someone else has another idea that I'm over-looking...
Pessimist: Oh, this can't get any worse!
Optimist: Yes, it can!