First make sure you don't have software such as vJoy or Smartpropoplus installed, they can mess with the USB input drivers.
From what you describe, it sounds like you might need to adjust the endpoint settings on your transmitter, similarly to the Taranis setup document.
https://drive.google.com/file/d/0BwSDHIR7yDwSOGhPMTFyWEpDVWM/view?usp=sharing
(Note that that document is written for the FrSky Taranis specifically, but you might get some ideas on how to make a similar adjustment on your radio).
Also, if the automatic stick detection gets it wrong during calibration, you can manually click the circle that you see is the correct one (instead of clicking 'OK').