Hi man. Exact same happened to me. When I boot up the FM3, it worked flawlessly then all of a sudden, the 3 on board switches stopped working so I cannot change to a new scene/sound. I restarted FM3, then its back to normal. My presets are quite simple and uses only 65-75 CPU.
I'm just practicing at home but I've experienced it at least 3 times to prompt to go back to FW 6.00. It's been a month now and not one instance of switches freezing.
If you use a single sound through out a song then it's no biggie but if you need to change from a loud distorted tone to a quieter tone (or vice-versa) then a freezing switch in the unit will be disastrous.