That's freaky. If you've renamed your bindings away from the default/custom name (I can't remember the lingo, but it's mentioned above and I imagine you know what I meanI wrote my post based on my own recent experience with that very thing. I launched the game without turning my Xbox controller on (even though it uses Microsoft's wireless USB dongle, apparently you have to turn the controller on in order for the dongle to activate, or at least I assume), and ED had reverted to the default keybinds config file (turning the controller on while ED was running didn't make it use my custom config rile again). That's when I noticed that I had to go through all four keybinds categories and re-select my custom config file in each.
I used to get exactly the behaviour you describe and it drove me nuts.
I do like JG but one minor gotcha is that if you use any plugins (this may happen in other cases too?), it disables itself every time a device is plugged or unplugged, including devices that aren't even used in the JG profile.Joystick Gremlin