I had similar problems when changing joysticks, it seems like the settings config file gets wonky. It may also be a problem when a joystick gets removed because it is no longer detected... although this was not my case. After deleting the settings.cfg file (this is a pretty big hammer as it also resets all your other settings) I was able to register my joystick axis. I think the config file gets some bad settings (in particular for pitch axis -- although this may just be a symptom of the fact that it is the first setting and is the most likely to get "multiple" and/or "changed" joystick configs first) and hangs before popping up the dialog to register the axis. Anyway, after removing the settings.cfg file, it started working. (Kerbal recreated a default settings file when I restarted it.) Hopefully, this can help the devs somewhat in diagnosing this bug.
