First check the B-17 configurator to see if brakes are set up in there, then check FSX controls pane.
Sorry but I couldn't find a box or option for the brakes in the B17 joystick configurator...
I don't actually know
there is one, I was going from memory
Did you tick (or un-tick) the reverse box in FSUIPC? I had the same
problem with the Spit too. As a test/check, in the B-17 with your feet off
the rudder pedals, does the word "Brakes" appear in the usual place on screen? If it does, then it's definitely a "reverse" issue. With my feet off the rudder pedals the brakes were ON, and when I pushed the pedals the brakes went OFF, reversing the axis sorted it out. The more I think of it, the more sure I am. I believe I used the "Aircraft specific" option in FSUIPC, but can't be sure as I used that for many, many aircraft.