I'm having the same problem trying to set up my Spektrum DX9 using PWM protocol with Mode II configuration with an Orange R1020X V2 receiver. It worked just fine with 15.09 and the transmitter settings haven't changed.
The first several steps of the wizard go OK, including recognizing movement of each stick separately, but the Flight Mode switch and the Aux switches are inconsistent.
When I move on to the step after centering everything, moving the sticks on the transmitter doesn't show movement on the computer screen, although the "Activity" bar at the top of the screen shows activity on whatever channel I'm testing at the time. Obviously, this prevents checking for the reversing function or anything further along the wizard.
The hardware setup on the vehicle hasn't changed from when it was flying reliably using 15.09 to set it up.
I've rechecked the channel and switch assignments on the transmitter, rebound it to the receiver several times, and the receiver LED indicates it's receiving a signal. When I disconnect from the Revo board and plug a servo into each output channel of the receiver, the servo responds appropriately to the stick/switch on the transmitter.
Is this a known problem with 16.09 RC2?
Is it possible to uninstall 16.09 and reinstall 15.09 until this is worked out?
Thanks