As far as I know, flatpak application data should live in $HOME/.var/app/<app-name> so I would suggest you move that folder to <app-name>.bak and run it with "fresh" config to see if it matters. This will ensure that any broken config gets "reset" and at least allow you o confirm whether it's something in your settings or not.
There's also a snap you could install to see if this is present with completely alternate source (though it's slightly older than than flatpak).
Other than that, nothing comes to mind on what to try...
