Hi BadBud,
More than likely your problem has to do with what aircraft you are flying. I'm going to assume you are flying allied craft?
The Allied planes do not have toe brakes in RL and Cliffs has them modeled as such. For instance the spitfire has a handle on your control yoke you'd squeeze with one hand to apply braking pressure. But the real kicker is the differential braking occurs by the control of the rudder. If you look in the lower left of your instrument panel you'll see a differential brake pressure gauge. So as you are moving the rudder left or right you'll notice more brake pressure / applying power has been applied to the right or left side via when moving the rudder and holding the brake handle down.
So basically you'll have toe brakes in Axis aircraft, but you'll have differential braking in Allied aircraft. So you'll need to assign a different key for the use of brakes for the allied craft as toe brakes will not work. Most people assign toe brakes as you normally would and use those for the Axis craft, then have a brake lever / keyboard button / or similar assigned for brakes in the Allied craft.
If you look through the controls you'll see a separate assignment for braking. This is what you'll need to use for Allied craft. It's not a problem with your controls, it's just how the planes really were.
If this isn't your issue, then disregard everything I just said
