I have a similar problem only with a twist... Every button works fine at the begining of the mission but after about an hour in the mission, it seems DCS forgot where I left the switch at.
For example, when coming for landing after an hour long mission, I lower the flaps 1 notch, nothing happens. I have to flip the flaps switch back up and down to MVR again for DCS to detect it. Very frustrating.
Oh and that is with or without sync hotas option ticked.