Are the 2x small SMD capacitors near the switches soldered well: test them and check for lifted traces as well. Otherwise check the circuit from the switch to the next component for broken traces.

Anyway it's not really a big deal that the programmer switch doesn't work as you don't need them when the logic board has been recapped.

I never had to press the reset/interrupt switches again after recapping my Mac portables while before it was always a pain and guess after how many times it would start...