My super tenere has also got the same problem with the CC, i have narrowed the search down to my front brake leaver. I am having some thoughts about the problem which i would like to share with you all.
Having read all the things that have been tried bij various people (and my own investigation) i think the micro switches are the ones to blame. The ECU expects signals from various components of the bike (depending on the type of switch it does or doesn not want to see a curtain signals, NO er NC as described earlier by MebGardner) These signals are checked by a watchdog timer, which usually is programmable by the factory or a programmer that can dig deep and knows his business. The problem, I think, is that let's say the component sends a signal every 0,10 sec and the watchdog timer checks every 0,15 sec if everything is normal. When he misses a signal he wil generate a faultcode and blocks the function.
Instead of changing out the very expensive components the problem could be solved easily with an software update from the factory. For example setting the timer at 0,25 sec. Then it needs to miss the signal twice before getting into action. This way it will ignore the "bounce" in the signal discovered by MebGardner. The factory can run simulations and test the correct timing, and making sure safety isn't an issue. I personally can't perform this but i am sure others (and Yamaha) can.
This way of problem solving is pretty common in my Job as a mechanic (mechanical and electrical) in a large factory.
Please let me know what you think and i apologise in advance if some sentences or words aren't right. English is not my first language.
Greetings