I was trying to report a similar bug when I saw this one.  I am having
the same problem with the top and bottom panels disappear when I open
any application.  For example when I open an application, it will always
open from the upper left corner covering the top panel.  If the
application uses full screen, the application will cover both top and
bottom panels making them not accessible.

My problem started after I tried to make Firestarter start every time I
turn on the computer.  The following are steps of what I did and caused
the panel problem.

After I installed Firestarter using Synaptic, I went to System ->
Preference -> Session -> Start-up Session.  I clicked on Add New Item.
A dialog box opened up.  In the command line I typed "Sudo Firestarter
--start-hidden" and then "OK".  I closed the Session Manager and reboot
my computer.  I noticed that Firestarter did not start after I re-boot.
So I used Session Manager to repeat the add new item several times. I
still cannot make Firestarter to start after re-boot.  Then I gave up.

After the above failed attempts, I opened Firefox.  I noticed that the
top and bottom panels disappeared behind Firefox.  So I tried to open
other applications and I found out that the applications always open
from the top left corner of the screen.  The applications also hide the
top and bottom panel.

This problem makes using Feisty very inconvenient.  Is there a
configuration file that tells an application where to open on the
screen?  Where is this configuration file?  Can I manually reset the
configuration?

-- 
Top and Bottom Screen Panels Stopped Working Properly in Ubuntu Feisty
https://bugs.launchpad.net/bugs/109760
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Bugs, which is the bug contact for Ubuntu.

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