@Wokkun Not sure if you got it fixed, but I had been having this issue for a long while now. I finally spent a few hours trying to figure out how to fix it. Here's what I did that I think helped fixed it.
Under the Steam/userdata/<a number>/1213210/remote folder, I deleted all the savegame files, leaving the save_game folder empty. From there, I went up to the 1213210 folder and edited the remotecache.vdf file to remove all the data within the first set of curly braces leaving
"1213210"
{
}
Then I closed the steam client completely (including the desktop tray). This is important, because Steam will keep the old content of the remotecache file in memory. From there, I started the game and loaded/played a level. Exited the game. Checked the remotecache file to see if the new Player_RA_settings_1.bin file was added, then opened the game again to see if it remembered my settings.
Let me know if it works for you or not.