I have exactly the same problem on XUbuntu 12.04:

- OS: XUbuntu 12.04, all updates are installed
- boot from USB drive (real installation, no live system); memory is o.k.: 8 GB 
flash drive; 3,5 GB free space
- computer: IBM T43, standard equipped, no special features; runs fine on 
Ubuntu 10.04 since years
- usage of Xubuntu 12.04 was o.k. for a few days; problem with synaptic 
password window occurred "out of the blue"
- I come around this problem by starting synaptic in the terminal

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https://bugs.launchpad.net/bugs/976638

Title:
  pkexec does not find any authentication agent

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