Just guessing, but with a software change and the issue still there, I would look closely at all the switches.
With the game in switch test, pound on the playfield with your fist and see if any switches activate.
Check all the switches (optos) on the vari-target. With the balls removed from the trough, you should only see one vari-target switch closed in switch test. Is that what you see?
If you're getting any phantom hits at all from the shrunken head optos, the idol optos, or the super optos, replace both sides of each with new ones.
I would also check the connectors on the opto boards under the playfield. Remove balls, put game into switch test, raise playfield and wiggle each of the connectors to see if any are lose. Two small boards.
Also, do you have display version 3.0? Doubt that would cause these issues, but you never know.