I had a semi-similar experience yesterday; had a fresh install of the Dev version, and deleted all my profile information to be doubly sure I didn't have anything of the old files, and went to rebind my joystick, and it kept crashing to desktop. Though mine was when I was binding the rudder controls.
I am using a Saitek x52, and what I had to do was do the controller Bind options, which has been reported that there are no text on them, and then I was able to bind the remaining axis'.
Again not a solution to the initial problem but a work around.