Where did you get your board? I have my Crystal Castles cocktail table with dual trackballs working with the two inputs. I had this hooked up previously as one trackball through player 2 and found that in cocktail table mode, the player two joystick would stop working sometimes. If I reached over and moved the player one trackball, it snapped out of it. I got a new dual support board and a second trackball and it works great now.
The only problem I had is that the trackball direction inversion did not work on player two. I had to switch the X and Y wire pairs.