I've just started using a new Pi3 using the 2018-04-18-raspbian-stretch image and have run into a few minor glitches. I am comparing it to an updated version of Jessie that I have been using. I manage both Pis by logging in using SSH and then starting a TightVNC server with the same simple command in the remote teminal session:
vncserver -geometry 1600x800 :1
In the Jessie GUI session when I go Menu|Shutdown I get the "Shutdown options" dialog and if I click on either Shutdown or Reboot I get a dialog asking for my password and after entering everything goes as expected. However in the Stretch GUI session clicking on either Shutdown or Reboot has no effect. I can still shutdown or reboot by opening a terminal and entering "sudo shutdown -h now" or "sudo shutdown -r now" or their equivalents.
Is this a permission thing? And where are they set in this situation?
After a bit of ruminating I hooked up my Pi to a monitor and took a look at the main desktop and had no problem with the shutdown dialogs. I then installed synaptic (an application that requires root privileges) and got the same authentication dialog as with Shutdown. Now back to logging in via ssh and running the tightvncserver and starting synaptic failed to even show the authentication dialog. I installed the tightvncserver the same way in both Jessie and Stretch and can't think of anything else that might be different.
[added after some more experimentation:
I've found some similar posts in various forums pointing toward a problem with policykit. Trying to start synaptic from a terminal started in the tightvnc session yielded the following
pi@Mrs-Lovett:~ $ synaptic-pkexec
==== AUTHENTICATING FOR com.ubuntu.pkexec.synaptic ===
Authentication is required to run the Synaptic Package Manager
Multiple identities can be used for authentication:
1. ,,, (pi)
2. root
Choose identity to authenticate as (1-2): 1
Password:
polkit-agent-helper-1: error response to PolicyKit daemon: GDBus.Error:org.freedesktop.PolicyKit1.Error.Failed: No session for cookie
==== AUTHENTICATION FAILED ===
Error executing command as another user: Not authorized
This incident has been reported.
If I use an X11vnc session or if I just use a monitor directly with the Pi I have no problem getting the authentication dialogs.
]
Also in Stretch, Menu|Shutdown->Logout causes the Desktop theme to change to Raleigh and the Icon theme to change to Gnome, but user pi is still the user and everything works the same.
Since there have been no responses here and following the advice of XECDesign ("That's probably a question for the forum, since it's not a Linux kernel issue. It would help to include the exact error messages.") from the github forums I'll open a new topic in the Beginner's forum with the title "Policykit problem in Stretch" and include a transcript of a session with the error messages.