I would say "Yes" because I had a bad ECM that held the PTO injector wide open and spraying like a jet cleaner. I swapped ECMs and the bike ran fine. That said, I would check the connections and make sure they are clean and do the tests in the Manual on Plug Number 4. Make sure the pins are clean and not wet. You could swap injectors to see how they are functioning. There is also a 5 volt test with the start button pushed and the key removed.
If you're encountering this problem at idle, I know the ECM is suppose to make the engine run on one cylinder which I think is retarded. I've checked the spark on both cylinders at idle so personally I don't think the ECM shuts down the spark. I'm no guru though. Good Luck !!