Settings resetting to default after closing Lutris

I’ve installed Pillars of Eternity (GoG version) on Ubuntu 23.04 through Lutris (flatpak). Everything works fine, however, as described on the title, when I close Lutris the game settings reset to default.
If I close the game and relaunch it without closing Lutris the settings don’t change (as it should be).
Has anyone had a similar issue or know a fix to it?
Thank you for any suggestion!