I'd first check... correct number of balls installed in game? check shooter lane switch

edit: check trough opto board, dummy (me, not you )

You can try to clean them with some ethanol on a q-tip. Also check the trough for any divots. This can cause ball count problems.

http://www.pinwiki.com/wiki/index.php?title=Williams_WPC#Trough_opto_boards

Inspect the trough boards for dull or cracked solder.

Check if the transmitters actualy transmit, use a camera to see the infrared beams.

I had this problem. If you recently added the deadworld mod you need to put that trough plastic inside the trough. It de-magnetizes the balls or something.

Or count all the balls and make sure you have the correct amount. I found one inside the machine pinned against the ball corner and put it back on the playfield. Turns out I had seven in the machine and it did the same.

Or do the trough inspection like noted above.

I am having the same issue. Originally the test report said I had a bad switch in the trough. Pulled that out and found a bad ir led that I fixed with solder. Now the test report is clear, but it's still kicking out 2 balls occasionally. Looks like I have a bad switch on the left ramp entrance.
Where is the transmitter board you replaced?

I'd try re-flowing the solder to the optos and board connector first. You likely just have a cracked solder joint from vibration.