I have a reproducible test case, but you need to set up for VNC (I have
a fresh 20.04 install, running headless, and this bug is a total PITA -
it's pretty much permanent. Note that it's worse than the screenshot
from comment #3 because the password is also viewable, and anyone can
come along, click the eye icon, and see my password). If you don't want
to vnc, see below.

In my case, I've installed the tigervnc server (tigervnc-standalone-
server).  Two changes to /etc/vnc.conf and you're good to go (note that
no custom xstartup is required):

# must do this to connect remotely
$localhost = "no";

# set to whatever your remote screen size is
$geometry = "3840x2160";

polkit has issues with remote access and pops up lots of 'Authentication
Required' windows. Eventually one will go in the top left corner and
stay there, with the described behaviour. I think, but I'm not sure,
that one way to trigger this is by hitting RET after entering your
password, rather than the Authenticate button. Note that you may have to
wait 10 or 15 minutes for another popup if the initial popups don't
trigger this bug.

I've added a local polkit policy to try to get rid of the popups, to try
to make a remote session look like a local session, which would
hopefully get rid of the popups, but this isn't yet working. The Alt
F2/r fix described above doesn't work.

If you don't want to run remotely over vnc, you should be able to
trigger this by changing the default polkit policy for an app you use.
See /usr/share/polkit-1/actions. A good one would be
org.freedesktop.color.policy, which is the one which traditionally
causes VNC problems ("create a color profile", etc). Find the 'allow
active' lines, and replace the 'yes' with something like
auth_admin/auth_admin_keep/auth_self_keep/etc. You'll then get the auth
popups when you log in, and various time afterwards.

-- 
You received this bug notification because you are a member of Desktop
Packages, which is subscribed to gnome-shell in Ubuntu.
https://bugs.launchpad.net/bugs/1824874

Title:
  undismissable, unclickable authentication dialog left on screen (top-
  left corner) after policykit authentication [pushModal: invocation of
  begin_modal failed]

Status in GNOME Shell:
  Unknown
Status in gnome-shell package in Ubuntu:
  Fix Released

Bug description:
  In disco, when policykit prompted me for a password in order for
  update-manager to dispatch instructions to aptdaemon to perform
  package updates, the password dialog remained on the screen after I
  clicked 'authenticate'.

  The window is not clickable, it appears not to even be a window -
  mouse presses are received by the window underneath.  The exception is
  that the 'cancel' button is active and receives mouse events - but
  clicking it does nothing.

  This may be a gnome-shell issue rather than policykit.

  ProblemType: Bug
  DistroRelease: Ubuntu 19.04
  Package: policykit-1 0.105-25
  ProcVersionSignature: Ubuntu 5.0.0-8.9-generic 5.0.1
  Uname: Linux 5.0.0-8-generic x86_64
  NonfreeKernelModules: zfs zunicode zavl icp zcommon znvpair
  ApportVersion: 2.20.10-0ubuntu27
  Architecture: amd64
  CurrentDesktop: ubuntu:GNOME
  Date: Mon Apr 15 13:14:33 2019
  InstallationDate: Installed on 2010-09-24 (3125 days ago)
  InstallationMedia: Ubuntu 10.04.1 LTS "Lucid Lynx" - Release amd64 
(20100816.1)
  SourcePackage: policykit-1
  UpgradeStatus: Upgraded to disco on 2019-04-11 (3 days ago)

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