Let me see if I can put this coherently: Programs that require super user authentication AFTER they have been launched (for instance,in the time settings applet, you have to sudo authenticate to update the clock, but not just to open the applet. Another instance is Ubuntu-Tweak, which requires admin rights for some of it's functions.)
A couple of clues:
This has persisted over a re-install.
I have a separate /home partition.
I can call the programs from the command-line using "gksu whatever".
I don't get a flash or any signal. Usually, nothing happens. Ailurus gave me a message "Operation is canceled because you refused authentication. Authentication is provided by system PolicyKit service. Ailurus does not know your password at all."
PolicyKit is NOT among my startup programs. Investigating further...
UPDATE: SOLVED Ubuntu-Tweak showed PolicyKit as starting; System/Preferences/Startup Applications DID NOT. So I copied the information from Ubuntu-Tweak: (First, check off "Show All Runnable Programs" and "Show comments") Auto-Start Programs/PolicyKit Authentication Agent, highlight it, then click "Edit" on the upper right. Then open System/Preferences/Startup Applications and click Add, again in the upper right. Just copy the information over from the Ubuntu-Tweak window to the Startup window you have open. Reboot. Enjoy.
Any other information provided on request. I'm using Ubuntu 10.04.1, all updates applied.