So I used the PKGBUILD and tarball from Arch and built and installed xdg-desktop-portal-gtk - that fixed my issue in the gtk apps I had installed via flatpak (gimp-devel, flatseal and tauon-music-box).
Assumably xdg-desktop-portal-gnome needs to be installed for gnome apps to work properly, but I don't use any so idk.
Steps to reproduce the problem
Install any gtk app like gimp via flatpak, launch it, close it, try again with xdg-desktop-portal-gtk installed.
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After
![after](https://user-images.githubusercontent.com/111146899/191281213-337df95e-ba3b-49e2-b0e3-ad12eafbda01.png)