Posting to add that I'm having this problem. While deleting settings.cfg partially works, it's not a complete solution. I'm using a Thrustmaster HOTAS Warthog and Saitek Pro Flight Combat Rudder Pedals. My main problem arises when I use the Thrustmaster TARGET GUI, which creates a single virtual controller out of the throttle and stick of the HOTAS setup. If I have this virtual controller set up, then none of my axis mappings from that device will be accepted by KSP. While I can map axes from the stick and throttle if they aren't mapped to the virtual controller by the TARGET software, that leaves me with significant difficulties mapping any button commands. KSP won't accept any button/hat/switch inputs from either device. I can manage a partial work around of this using Xpadder, but that doesn't handle the throttle switches very well at all. If the controller name issue was resolved, then I could use the TARGET software, which would allow me to configure all of my controls as I would like. To be clear, I can assign axis mapping in KSP to the Saitek rudder pedals, and to the Thrustmaster stick and throttle when they are separate devices, but I can't assign any button mappings to the stick or rudder if they are separate USB devices. The pedals have no buttons to map. When the two Thrustmaster controllers are assigned to a single virtual controller through Thrustmaster's TARGET software, then I get the problem repeatedly reported here; axes will be recognised by KSP, but they can't be saved. Also, any time I want to try a different controller config (e.g. TARGET on/off or additional devices plugged in or unplugged), then I have to delete the settings.cfg file and start again with my config from scratch. Otherwise I get the other oft reported problem in this thread and the axis assignment window doesn't come up at all.
