I had that issue on gentoo running systemd with xfce4. Even though
xdg-desktop-portal and
xdg-desktop-portal-gtk portals were installed and running, gnome-boxes file selection window was not working. The solution was to set gtk portal by default:
create
~/.config/xdg-desktop-portal/portals.conf:
[preferred]
default=gtk
org.freedesktop.impl.portal.FileChooser=gtk