One odd thing I have on my MB, is that with LED's installed by the left outlane, I get an error when I turn the game on, that the left phantom flip is out - I switched bulbs back to regular, and its fine - so the LED "fools" the opto - the phantom needs the inlane speed, opto and eddy board to work together for the software to pick up the "event". SO, if you have LED's, it might be affecting the opto. Else, you can test and adjust the eddy using the link of paisley pinball below.
Check if Eddy board might be bad, try switching the right to the left. To buy a new one is $45 here: http://www.marcospecialties.com/pinball-parts/A-18543-1
diagnostic help....from RGP https://groups.google.com/forum/#!topic/rec.games.pinball/hxZocBaOGp0
I had trouble with the sensors some time back. I remember adjusting
them according to this site because they were so finicky. I had to
keep the play field propped up to check the LED on the eddy board,
then I would keep adjusting the resistor until it worked. I had the
same problem, and this worked for me.
The Phantom Flip is driven by software, there is no hard trigger.
It measures the speed of the ball using three sensors - the inlane
switch; the opto; and the eddy sensor.
If any one of the three is less than perfect, it will never enable the
phantom flip for that lane.
One thing to check: watch the LED on the eddy board, and flip the
flipper. If the LED flashes, you'll have a hard time with it. A new
controller chip will help a lot.