That bug has been opened on https://launchpad.net/distros/ubuntu/+source/gnome-panel/+bug/39856

"Happens when the box to fit the panel to screen width in its properties dialog is unchecked:

After restarting X the panel that is supposed to be at the bottom of the screen is right in the middle of it. The panel stays there until I check the box to fit the panel to screen width in its properties dialog.

Looks like this:
http://tobias-fink.net/Files/Upload/Gnome-Bar.png
...
> Thanks for your bug.

from bug #44333:

"When I unckeck the "expand" button for the default bottom panel. Log out and log in again; The panel which should (still) be appearing at the bottom of the screen, places itself just under the top panel. This behaviour was also found in the 'previous' version (Breezy).

Steps to reproduce:
- Create a new "desktop" user
- Log in to Gnome with newly created account
- Right-click bottom panel "Properties"
- Uncheck the "Expand" button
- Hit "Close" button
- Log out of session
- Log back in to Gnome again with same account (new one)

>> Now the bottom panel places itself just under the top panel

Note: When you try to set the orientation back to "Bottom" for the (previous) Bottom-panel, It refuses that and 'automagically' reverts back to "Top". Except when first checked the "Expand" button, it allows to set the orientation back to "Bottom"."
...


Something similar happens when switching the panel to be on the left or right:

  1. Setup panel to be 'top' and unset 'expand'.
  2. Re-open panel properties.
  3. Set location to be 'left' or 'right'.

The panel now appears in the middle of the screen. Then do

  4. Set 'expand',

and the panel goes to the left or right as it should have done rightaway."