Just to +1 DCFan's suggestion..
I know it, logically sounds weird because the switches seem to work in switch test but I've also seen this with my old Tron Pro, a friend's AC/DC, my Star Trek Premium. It must be super sporadic, just enough to throw the ball count algorithms off. Pull both boards off the trough, reflow them, add them back. Be sure not to bridge the pins with solder.
I'd bet you lunch that fixes it.