Mine has been doing this for 3 years.
Today I finally brought it to the garage, they checked the shifting motor, change the angle sensor that was fill with water (my quad has never been in the rain nor in a pool, simple washing with a regular hose with limited pressure) They checked everything. Mechanic went for a test ride, still the same problem but less intermittent.
I left the d... thing there and bought a new one with foot shifter. I only had 540 mile on it.
They do no seem to know what cause the problem and told me it is very rare. I read a lot of those problems on the web.
Hope you find your problem. By the way, have you checked the front big connector under the hood between the 2 shocks, and the big gray one under the seat right side for moisture?
Good luck to U.