Hardly ever on the score motor.. more likely on the bonus unit. did you pull this apart and reassemble?? If you did, did you make sure it aligned as before?
If you havent touched this then the contacts and wipers may not be making good contact. Bonus units should be taken apart, cleaned and reassembled.. they are part of the logic of any EM game. Often over the years these got lubricated or sprayed with WD40 etc... this gunks up and prevents the contacts from making properly. You need to make a scrape with a screw driver or similar on one of the legs and also a mark where it sits on the contact board. Take all this apart, clean with meths and reassemble. Dont use a marker pen to make your marks as meths will remove this and youll be up a blind alley ( reckon weve all done this at some point!). Clean all the brass buttons with meths, make sure it all moves freely and reassemble. The brass legs should sit directly on a tab on each click.. there is some 10mm adjustment that can be made with these by lossening off the mounting screws. Align and tighten the screws.
Do all this and you should get your bonuses registering.

What a bonus unit does is allow current flow to a set of switches... all tabs sit high on voltage and as the wiper moves over them it runs this circuit to ground.. this will pull in a relay further down the path, which then allows scoring, bonus lights to work, etc. If this is not working properly then youll hear clicks as it turns around but there is no path to ground and so you dont get the points you are meant to.
DDtoys i believe wrote a piece here on AP about pulling these apart and reassembling in Tips 101.. go look it up and follow it through.

Best of luck and report back any success.. we love hearing this kind of news!