The circuit that drives the motor is CPU bus -> power driver board -> HCT273 latch -> Q32 transistor. There is not a single pin on the CPU board that could fail that would only affect the canon motor.
There is, however, still a possibility that I can give some info on. A friend's game (Premium) had (maybe still, I'm not sure) an issue where sometimes the cannon would work, sometimes it wouldn't. If it worked the first time, it would continue to work until the game was turned off again. If it didn't work the first time, it would never work until the game was turned off again. It was like the software was looking for something to happen either at boot time or on the first use of the canon, then determining whether the cannon was functional or not.
If your game has an issue with that detection that is related to that CPU board, you might be experiencing the same result, only yours fails every time. Of course, it could be completely unrelated.