Well, we got the bad news from Boat Depot...it was not something simple or cheap. Apparently the engine's EMM is bad, and must be replaced at a cost of $1,300. That's about 20% of the cost of the motor when we bought it new. Unfortunately, the motor is out of warranty, so we'll have to cover the whole cost.

We were not able to get any definitive answer as to what caused the problem, or how to prevent it in the future. We're OK with paying for the repair, but it would be nice to know that it won't happen again in 3 years. BRP Tech Support suggested that perhaps our battery caused the problem (too small, and a deep cycle, rather than a starting battery). But considering that the motor has never had a problem turning over (once we got through the water in the fuel issue), and can run without a battery, it seems unlikely to us that those could cause the EMM charging circuits or software to go south.

Remember that the motor runs fine, even with the defective EMM - it just doesn't charge the battery.