Weird stuff!
Now I do recognize that something changes between first time you look at the Axes via Options, Controls, and the next time. The sliders I use for trim (on a Bodnar board) do not show the same response the second time I look at the controls. It all seems much slower - but still, they do work.
Once in cockpit, no issues.
But, this fact does not help you one bit.
You could try and re-install DirectX (Run DxSetup.exe as an administrator, from this folder: C:\Program Files (x86)\Steam\steamapps\common\Steamworks Shared\_CommonRedist\DirectX\Jun2010)
And maybe have a look at the input section of DxDiag?