On Windows machines this is usually caused by not having done a Windows calibration of the USB input device in 'Devices and Printers' in the Windows control panel.
If you have done this or you are using Linux or OSX then you can click the calibration button in USB setup and then find the axis you are trying to assign.
Once you have found the axis turn up the sensitivity slider so the axis is throwing further and then try to assign the control again.
In most cases increasing sensitivity will allow the axis to be detected, make sure you turn sensitivity down to normal levels after doing this as otherwise the quadcopter controls will be over sensitive.