I had some trouble getting gnome-boxes to work on my Ubuntu machine. It turned out to be due to having an encrypted home directory, see this bug report.
The thing you need to do is to make sure that
~/.local/share/gnome-boxes points outside of your homedirectory. I
made it a symbolic link to /var/lib/gnome-boxes, like this:
$ sudo mkdir /var/lib/gnome-boxes
$ sudo chown $USER:$USER /var/lib/gnome-boxes
$ rm -rf ~/.local/share/gnome-boxes
$ ln -s /var/lib/gnome-boxes ~/.local/share/gnome-boxes
Afterwards, you need to reset the storage pool for virtual machines:
$ virsh -c qemu:///session pool-undefine gnome-boxes
And done!