Forgive me for waking up an old thread, but I have the same problem as the OP, and I can't seem to do anything to mitigate it.
I have Saitek combat rudder pedals, the problem is with the toe brakes. If I calibrate them in Windows everything looks fine. If I calibrate them in AFS2, it looks a little weird. With no brake demand, the slider display seems to be full negative, but as soon as I touch the toe brake it jumps up to zero. In game, this has the effect of applying 50% brake even when you make the lightest possible touch of the toe pedal.
I tried moving them to 50% when the AFS2 calibration dialog asked me to center, but that did not have a beneficial effect.