This is hardware-related. Unfortunately, the wires CH uses in its pedals are very thin and brittle, and over time they're prone to snapping. Once a wire snaps, the function that it corresponds to ceases working. I lost both toe brakes and one of four rudder axes (right up, right down, left up, left down being other wires that can potentially snap in addition to the toe brakes).
If you feel confident opening up the pedals, it's not very difficult to mend the broken wires. I managed to fix my rudders myself, and they're like new again. If you're in the least bit worried about dealing with the innards of the pedals, contact CH immediately, and ship them back for replacement.
-- Todd/Leviathn