Only five members with this game, so maybe this post hasn't been seen. I don't have the game, but looking at how it's set up, the three switches on each side leading to the flipper would all have to be correctly working 100% for for the Phantom flip to work. Have you checked those are working correctly?
I noticed some replacement parts on pinbits, (replacement eddy board and microcontroller) the other day, made me wonder if those might be problematic on your game (I assume a common problem for them to have remade them)?
http://www.pinbits.com/index.php?main_page=index&cPath=13_7&zenid=g3d3p8as5fdge6nrnbmsa02tf0Sorry I can't help any more, I don't have much experience with this game.
