This is usually caused by not having configured your controls in USB setup.
Customers should assign their tx in USB setup, calibrate their axis and then finally assign their controls. It is this last step that customers usually forget to do.
In the USB setup window the (yellow) buttons on the far left of the screen alongside the different flight control names (throttle, roll etc) should have an axis assigned, if they do not have an axis assigned then although you may have calibrated your input channels you have not assigned anything to them. Once you have assigned controls the quad copter in the top right of the screen should respond to your transmitter stick inputs.
Now if you go to flight mode you should have full control.