I updated from dapper to edgy yesterday and I experienced something
similar: Several configuration apps like update-manager and software-
properties are being launched via gksu instead of gksudo. Nevertheless,
a gconf-entry for sudo-mode was not installed. I had to explore the
problem by myself and added the gconf key manually.

This issue should probably be checked inside some Ubintu base package!!
Ubuntu will ALWAYS want to use gksu in sudo mode no matter what so some
config script should make sure that the sudo-mode switch for gksu is
properly set in gconf!

Normal users would almost certainly give up on this because gksu will
keep giving them "wrong password" errors! I recommend to shift the
importance of this issue.

-- 
gksu not in sudo mode
https://launchpad.net/bugs/27636

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