USB HID Joystick - X&Y Axes not responding, but other axes work

I'm new here and this is my first project with Arduino. I'm able to build and deploy this successfully on a Leonardo Pro Micro using Arduino 1.6.5

https://github.com/Cryocrat/LeonardoJoystick

The problem is all the axes work - move randomly as expected, but the main X & Y ones. I don't think it's the board, as I have the same problem with other boards as well. I suspect that there's something special about USB HID descriptor for X & Y axes which is preventing it from working.

I think I found the problem. There seems to be a bug around the implementation for the Arduino Leonardo in the IDE. If I change it to Arduino Micro or Arduino Yun, it works.