OK. So, the targets work normally, but once you go through the "return to lane" gate, the targets start doing the funky "any drop lights special"? Is there any other impact, like it also lighting (or strobing) the "reset drop targets" lights when you drop any drop target?
That switch (Rollunder, #52), shares the same row (Strobe) as the red target (#32), top kickout (#42, which collects the bonus), the star rollovers (#12), the third rollover lane (#22, lit when bonus multiplier is X3), and the Right Coin Chute (#02). That strobe line is on connector A1J7, line 4, the wire colors are supposed to be Black, Orange, Orange.
First thing to check is to see if the rollunder switch attached to the gate is correctly gapped. It should only be closed when the ball passes through the gate, and reopen once the gate is cleared. It should not close if the ball doesn't make it through the gate - there isn't any real ambiguity, if the ball doesn't have enough momentum to pass through, it won't trip the switch and will be pushed back into the playfield. Make sure the spring isn't binding and holding the switch closed.
Do you have the manual for the machine?