I've tried the following workaround, and it works for me across a
session logout/login.

Short:
Use gconf-editor to change the value of 
/apps/panel/toplevels/bottom_panel_screen0/y to the vertical screen resolution.

Notes:
I ran gconf-editor from the terminal.  There were other keys for 
bottom_panel_screen1 and top_panel_screen[0/1] visible, but I tried this one 
first and it worked for me.  When I changed the value to the current vertical 
resolution it appeared to invoke some magic, because the value automatically 
adjusted to put the panel at the bottom of the screen: I typed "1024", hit 
return, and a split second later it said "975" where it used to say "1024".  
The calculation appears to be ((Y resolution - Panel size) - 1).  Panel size is 
visible in the panel properties dialog.  As soon as the new value was entered, 
the panel moved to the new position, and I quit gconf-editor.

Thanks:
Originally found in dbloom's post at 
http://ubuntuforums.org/showthread.php?t=117997

-- 
Panel in middle of the screen after reboot when not full-sized
https://bugs.launchpad.net/bugs/39856
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