Thanks for the replies so far. I was going to call or email JJP tomorrow regarding this and I've scanned over the IO board and not seeing anything obvious.
As for the loose connectors or short, its possible and I've gone over every harness but not finding anything yet. The strange thing is I can't seem to isolate a consistent issue. Sometimes one target or pop will initiate crazy behavior and later it will be a different one. The flippers work when it is not "possessed" and then they stop working when it decides to flip out. I'm guessing it is activating a tilt as part of its craziness but not calling or showing tilt.
There is no consistent pattern that I can find other than suddenly everything (switches, flippers, coils) will go dead and then it freaks out for a bit.
I'm hoping LTG has seen this before and can shed some light on the situation. In the meantime, I have a call into a buddy of mine who does some pinball tech, maybe I can pay him to figure it out...