I had this problem earlier (months ago) too. No idea why this happens. I even filled a bug report and ask them to store the config in the cloud, if they do not already.
When Horizon came out, I upgraded and I was happy because all my settings were there. I hope it will remain this way. There are way too much keys to configure them all the time. At least they should a manual export / import feature.
I'm not sure if it's changed but early on in the beta and just after, we found that the control settings would just wipe occasionally and I found that if you have any controller change between setting up the custom settings originally and then starting the game they would blank.
In order for everything to stay as you want it then EVERY controller you had plugged in at the time of setting up has to be plugged in when you start the game AND (on my system anyway) has to be plugged into the exact same USB port as it was at set up. If you start up with say... your pedals not plugged in... then that whole profile will fail to load and revert to custom blank.
To get it back just exit the game and plug stuff in then restart the game.
I have found just recently since Horizons came out that I prefer to use my xbox 360 controller to steer the SRV but as the controller is wireless and also goes to sleep, if it isn't alive and working at game startup then my profile doesn't load.