I'm not quite sure I get what your saying, but when you go into the select joystick choice area you would click on "left Brake", then "right Brake" then make sure your pedals are clicked on in the center, and then on the right side (joystick input) of the screen click on "x axis" and "y axis" for each respective break position.
This choice of "x axis" and "y axis" does seem confusing, but it is the x and y axis for the brake and should not control the same x and y axis your stick does.
I hope it's as simple a fix as that.
When done make sure that when you calibrate, at all times, you also depress each toe brake to make sure they are calibrated also.
Ranger Bob