Arkuz, I had a similar issue, except instead of a particular bonus not scoring, it was the 3,000 bonus light not lighting up. Same thing: I'd lift the playfield, and presto! The light would be on.
I found my problem to be a loose relay stack under the playfield in the trip relay bank (the one with the large reset bar under the joker rollovers). Tightening up the stack and filing the contacts clean seemed to have resolved my problems.