I'm using a VKBSim Gladiator II joystick, and the autobrakes work fine in FSX boxed (also in FSX-SE), so maybe the problem is with your pedals.
When landing, I can set the Autobrakes to any setting, 1 through to Max, and they work fine (as in brake hard on Max, brake gently on 1).
I have not had to change the settings in the aircraft.cfg from auto_brakes=5.