A problem similar to this has been posted on this forum before. Double check the switch wire colors and location. I am fairly sure the manual has this information listed incorrectly. Use the game diagnostics to figure out what is actually correct. You can determine switch state from test 07 - switch edges.
Note that lock #1 is the LOWER lock as it locks first despite what the manual location shows. Lock #2 is the upper lock as it locks second. There is no switch for the third ball when it locks. The game knows that the three balls are there based on lock #2 and the third ball passing through the second ramp diversion and subsequent switch.