From Bugzilla Helper:
User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020625
Description of problem:
In the Limbo beta, using metacity with sloppy focus, userhelper password dialog
boxes have a tendency to very very quickly drop below other windows. In some
cases, the dialog grabs and holds keyboard focus (though not window focus).
To solve this, the userhelper dialgs need to be set as "Always on Top" when they
Version-Release number of selected component (if applicable):
Steps to Reproduce:
Run any program that uses userhelper wrappers. Do this preferably from a gui
tool (nautilus or a menu) with windows open. The userhelper dialog will drop to
the bottom unless the mouse happens to be where it pops up.
Are you using autoraise? If so, then this is unavoidable.
Consider the situation where you have two "always on top" windows which
overlapped (fairly likely, given that userhelper dialogs are always centered).
The window manager would have no way of knowing for certain which belonged on
top at any given moment, and Bad Things could happen.
I'm going to mark this WONTFIX because the GUI toolkit doesn't offer a standard
ALWAYSONTOP hint, I suspect for this or a related reason.