When machine is turned on and in attract mode, you can add credits, change the volume up and down and enter service mode via the coin door buttons. So obviously those are hooked up and the switches are working correctly.

Basically, once in service, you can not change the menu items with the coin door switches or the flipper buttons.
The start button will work and you can go into test and switches but that's it. You cannot move left or right in the menus.

The CPU, Driver and DMD Driver have been swapped out. The CPU and display ROMs have been upgraded to 5.00. The coin door has been swapped out.

I can't think of anything left to try. It does have a RAMTRON memory IC in it. Will try swapping that back to a battery pack as I'm ALL out of ideas.
Any help would be appreciated!

Just put a 6264 ramp back in with a battery pack and same issue.
AAARRRGGGHHHHH!

Solved.
The dolt that replaced the start button before we got it wired it in wrong. They had the ground on the wrong lug with no diode.
It's still weird that the buttons would work normally when not in service mode.
All is working now. Maybe this will help someone someday.