I do not quite understand the initial description, but if I interpret it correctly, is bug #41623 a duplicate of this one?
https://bugs.launchpad.net/distros/ubuntu/+source/firefox/+bug/41623 -- Popup doesn't gain focus after first open https://launchpad.net/bugs/33840 -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
