@RayN - I have tested on my skid steering rover with 3.1.1 and I can ARM no problem. Remember that disarming doesn't work on skid steering rovers as it means you rover would turn around in circles whilst trying to disarm.
@manulrk - I tested on my standard Rover with my standard setup and I can arm and disarm. I need a log file from you to investigate further - the one you posted previously is in an odd format - a tlog would be better. I assume you have changed the RCMAP_* parameters to reflect your changed channel setup?