Settings resetting to default after closing Lutris

Hello!
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!