If you had moved the machine recently and now doing a factory reset, the phantom flips don't work until the game see's the ball enough times pass over the sensors, and one side will start first then followed by the other.

Remove the glass, start a game grab the ball press the flipper button and toss the ball up over the the ramps once the phantom lights are lite, keep doing this several times (more then a dozen if I recall) and it should start to fire up providing everything is in order as you already checked.

Make sure all three phantom flip lights are lite before tossing the ball through the ramps for the flip to happen. Start at the enter switch so it registers it all the way through, if you skip a switch that received data may not process the sequence for the flip.

In addition I'm sure you checked but make sure A.2 24 "Disable Phantom Flip" is set to NO.

That's what I have been saying about the ball path, the machine should see the sequence of travel from start to end on all the inline switches leading upto the sensor or it might not trigger to sequence. So pull the glass, hit the flippers a few times light all the phantom lights, then hit the flipper buttons again and toss the ball from the very beginning of the its path the ramp entrance and allow it to run over all the switches up to and including the sensor board right to the flipper, then grab the ball and rinse and repeat.

I'm not a 100% sure if you need to hit the flipper button at all, but I did when I was learning my phantoms just to be on the safe side like a real game situation, then I tossed the ball through its path. Now I'm pretty dam sure it has to hit all the switches in sequence for it to learn. Like I said I knew it took like a dozen or more games before they started to flip on their own.

You did check that A2.24 is set to "NO" as well correct.