I have a similar problem (current version of Hardy), which may be the
same issue as here, only with gnome-terminal.  If I save my gnome
session, a terminal window in the upper left corner is taken to have a
geometry "100x32+5+24", as found in the saved session file
(~/.gnome2/session).  The +5+24 corresponds to the width of the border
and title bar.  If I open up several terminals in rapid succession, with
a script such as:

gnome-terminal --geometry 100x32+5+24 &
gnome-terminal --geometry 100x32+5+24 &
gnome-terminal --geometry 100x32+5+24 &
gnome-terminal --geometry 100x32+5+24 &
...

the windows will randomly be placed in the upper left or +5+24 from the
upper left (except the first one always seems to be upper left).  The
randomness disappears if the Compiz "Window Decoration" option is turned
off (so windows have no border/title bar): all windows are +5+24.

I suspect this is a timing issue between placing the window and adding
the border/title bar.  Adding a border to an existing window seems to
shift the window to maintain the position of the corner, but I do not
think there is any shift if the border already exists when the window is
placed.  So it seems the final position is going to depend upon which
action is performed first: placing the window or adding the border.
Maybe the order of those events is not fixed?  (This is only a guess at
what is going on.  I don't know much about the internals of Gnome and
Compiz.)

More details here:  http://ubuntuforums.org/showthread.php?t=894503

I don't know if this is the same problem as the one Danny Baumann links
to.

-- 
nautilus windows position changes each time the window is opened
https://bugs.launchpad.net/bugs/155101
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