I have a brand new 2021 212XD and am having the same issues. Just yesterday, we had a dangerous incident that could have ended badly but luckily no one was hurt.
Brief history. I purchased the boat this spring and put it in the water in May. Within the first 10 hours, I experienced the same issues described in this post. My drive paddles would occasionally not work or only the starboard engine would engage. I was able to temporarily solve the problem with a hard reset of turning off the batteries. I also got some of the warning messages mentioned here. I took the boat to local dealer. They had heard of this issue once before and it was caused by a loose wiring harness from what they told me. Anyway, they kept my boat for 2 weeks, could not recreate the problem or find any loose wiring harnesses and returned it to me (they also completed the 10 hr service). Over the next month, the problem happened occasionally - enough to be irritating, but not enough to make me want to put it back in the shop for weeks. Until yesterday.....
We took another family out on the lake for the day. Upon returning home, I was docking the boat with the paddles. Driving straight into our single slip dock (double decker aluminum dock). I was going very slow and half way into the slip just coasting and looking for the rope - suddenly the right engine engaged fully. My hands were not touching the paddles at all. We shot forward, hit the front of the slip and the front of the boat came out of the water, riding up on the dock. By the time I could shut down both engines, the boat was about 1/3 out of the water and the bow struck the stairs going up to the top deck. Once the engines shut down, the boat slid back into the water and out of the slip. Thankfully no one was hurt, though everyone was fairly shaken. My dock took some damage. My fiberglass on the top of the bow is damaged and the hull is scuffed. No leaks. Getting it towed to the ramp tomorrow, and on a trailer so I can take it back to the dealer. All in all, I am thankful that it was not worse, but I no longer trust that boat.
Any advice on how to approach this? Call Yamaha? Just deal with the local dealer?