You need to go through the FAQ, you need to UNBIND all axis on any controller that won't be used by it in WOFFKeys program. Save as you go. Access via workshop Re Map Keys/Controllers button.
i.e. take rudder off your stick, and then do the same forr the pedals. Unbind all others unused etc.

DX9 off option is really just for testing, something sounds screwed there somewhere. Also best to leave aircraft on "5". Make sure you install DirectX9 fully exactly as the step by step in the FAQ section 4
The FAQ is on our website, support page.