I'd test that transistor first, especially if this only started happening after you installed the new board. TURN OFF THE MACHINE TO TEST THIS. Put your meter to diode setting. Put the red lead on the big metal tab of the Tip36c and the black lead on each of the outside legs. You should get .4 to .6 volts on either leg. Put your black lead on the center leg now and you should get a 0 reading. Next put your black lead on the left leg and move your red lead to the center leg and again you should get .4 to .6 volts. Now keep the black lead on the left leg and move the red lead to the right leg and you should get .2 volts. If you get readings outside of those numbers, the transistor is bad and needs replacing.

Also, make sure the associated diode for that coil on the board is good.

Other than that, make sure the tieback wire on the little drop target coil is still in place. This probably isn't the cause, since it would most likely cause issues regardless of the knocker being plugged in, but it doesn't hurt to check. This thread explains the tieback wire:
https://pinside.com/pinball/forum/topic/sttng-tieback-clarification#post-4915211