You've got a switch that is responsible for resetting the score reels that is not making contact. The switch will be on the reset relay. It will be on that relay in the head. If the other reels are resetting properly it is not the score motor. It's that one switch. The score motor is running because the zero position switch on the reel is telling the score motor that the game is not reset to zero.
Make sure all the wires are solid to the reset relay. The bane of EMs is the switch which looks like it is making but is not. The contacts might be dirty. You might also have a broken switch blade on the reset relay switch. In that case you'll need to either take the switch apart and see if it is broken and replace it if it is. You can jumper from the solder tabs on the switch blades directly to the business end of the blade and that will also tell you if the blade is broken.
Since the game will play when you manually reset the reel to zero the zero position switch on the reel is good. And since the reel plays properly in game play the reel switches themselves are good also.