In my case importing any systemwide package installed causes this warning:

jarek:~/dev/cruncher$ PYTHONPATH=$HOME/dev/cruncher/cruncher/lib python
>>> import cruncher
>>> import pkg_resources
__main__:1: UserWarning: Module cruncher was already imported from 
cruncher/__init__.pyc, but /Users/jarek/dev/cruncher/cruncher/lib is being added 
to sys.path
>>> 
jarek:~/dev/cruncher$ PYTHONPATH=$HOME/dev/cruncher/cruncher/lib python
>>> import cruncher
>>> import psycopg2
/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-
packages/psycopg2-2.0.11-py2.5-macosx-10.5-i386.egg/psycopg2/_psycopg.py:3: 
UserWarning: Module cruncher was already imported from cruncher/__init__.pyc, 
but /Users/jarek/dev/cruncher/cruncher/lib is being added to sys.path
  import sys, pkg_resources, imp
>>>