Workaround found on Ubuntuforum:
http://ubuntuforums.org/showthread.php?t=342775

To manually save my panel layout once:
gconftool-2 --dump /apps/panel > panel_layout_1280_800.entries

and restore the layout after switching back from a different resolution:
gconftool-2 --load  panel_layout_1280_800.entries

-- 
Applets do not scale well with changing resolution
https://bugs.launchpad.net/bugs/36189
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