That's so ironic.. I currently have the exact same problem.. My machine is in free play mode, and the first problem I noticed was just that I couldn't start a game SOMETIMES.. Then, I notice that I can't adjust the items in the config mode, but hey.. I'm no expert, maybe i'm doing it wrong, but then I did the switch test, and found that it's the whole 2J2-9 column.. Tilt not working, credit switches, etc..
I think I've noticed (or it's my imagination) that the pin 9 on that connector is actually a little taller than the others, so I was going to pull the board off and reflow the pin on the back of the board. I expect this will work because my meter shows the wire is good, even when it's not working for gameplay.. Interesting that someone else had the exact same pin bad...