Interesting....
I have a similar problem with my Devil Riders... everything works in test mode, but in game mode, ball does not kick out, bumpers are dead etc. I have switch inputs to the board but no output.
I ran Leons test program for zaccaria and all switches strobe as normal BAR the output for TR3 which is in reverse.
Yet TR3 tests fine and is installed correctly... have replaced the 4028 that feeds this also, but no luck.
You can see now why i didnt reply any further on this thread... i have almost the same problem!