Confirmed on Ubuntu 8.04 RC.

A partial explanation for all this: The main issue is funky "Always on
Top" behavior. The authentication window grabs keyboard and mouse input
to itself, and it will sometimes appear behind other windows even though
it ought to appear in the foreground. That said, this particular bug
definitely seems to be related to the clock applet itself.

The clock applet's calendar/weather thingy is always on top. The Clock
Preferences window becomes "always on top" only when the clock's
calendar is expanded (even though right-clicking on the Clock
Preferences titlebar shows the Always on Top option is never checked).
In Gutsy this is innocuous, as there's not much to the Clock Preferences
window. In Hardy, however, clicking on the Time Settings button spawns
the Time and Date Settings window directly behind Clock Preferences.
Clicking "Unlock" on the Time Settings window will sometimes spawn the
"Authenticate" dialog hidden behind the other windows. It also grabs
mouse and keyboard input so nothing can be moved (I think this is
described in another bug). When the calendar is not expanded, the Clock
Preferences window is not always on top. Manually setting other windows
to be always on top allows them to appear in front of the Clock
Preferences whether or not the calendar is expanded (assuming your
keyboard and mouse aren't locked).

-- 
Setting the time using the clock applet, shows authentication window below time 
settings window
https://bugs.launchpad.net/bugs/200036
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