@zorglub yes it is indeed because you installed the flatpack version of steam. I recommend you delete that and any leftover steam files
(do not attempt to have a flatpak steam simultaneously with a native steam that is a terrible idea)
if you want to avoid redownloding the games you downloaded, you can take the folder in : steam called "common" that is under "steamapps" (if you right-click on the game in the steam library you can open the folder where the game is installed, then by going up one folder you'll have the "common" folder.) you can move that folder to another place, (say Documents) and then delete steam flatpak and install steam as a native.
when you are here : https://store.steampowered.com/about/ it gives you the right file.
you can run it by right clicking in empty space in the folder you downloaded steam to then selecting "open in terminal" and in the window that pops up, type in :
(I'm assuming you're on Pop_OS, ubuntu, mint, kubuntu, Zorin,... basically debian based. if not and you're on Manjaro or something like that, you'll have to do something else like
sudo pacman -S steam )
sudo dpkg -i steam_latest.deb
(you'll need to type in your password)
then follow the steps and then you'll be able to run steam from your start menu.
make sure to enable proton for all games in the options (steam was completely reinstalled so you need to do everything again)
then you can close steam, move your "common" folder to :
then start steam back up and start the download for the games you previously had installed.
steam will recognize the games are already in the right folder and simply "discover" them instead and then they'll be installed.
then you can try again by giving steam the run arguments I talk about in my video
run FA once from steam, go fetch the run file and put it in your FAF install dir and point to that in the FAF options.
and you should be good to go.