I had a similar issue after installing a cpr playfield. Partly, it seemed, with the tension caused by the spring steel flap where the ball emerges. Occasionally the ball would get kicked along the underside wireform but it didn't have enough velocity to pop out onto to the playfield.

I upgraded the coil strength, trimmed back the end of the chaffed wires and used new solder, and I just slightly tweeked the metal flap up and the problem went away. Make sure that there are no obstructions, including the range/arc that the end of the metal flap has to bend into.

Edit...I also suggest temporarily removing the metal arch above the shooter lane to see if that might be rejecting balls. Its the easiest first step. Its been a while since I sold it, so I may be mistaken on this element of the prolem.