sudo mv /usr/lib/pymodules/python2.6/pygments/__init__.pyc 
/usr/lib/pymodules/python2.6/pygments/__init__.pyc.broken
sudo update-python-modules python-pygments.public

made the warning go away

-- 
Spurious "Module ... has already been imported" warnings
https://bugs.launchpad.net/bugs/500621
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