i don't know my python innards well enough to fully follow all the ways 
that you can mess with imports, but i suspect that this file: 
http://code.google.com/p/googleappengine/source/browse/trunk/python/google/appengine/tools/dev_appserver_import_hook.py
 
which specifies a hook that is passed as part of the environment to 
LoadTargetModule() from 
http://code.google.com/p/googleappengine/source/browse/trunk/python/google/appengine/tools/dev_appserver.py
 
is what is over-riding the web2py over-ride of the __import__ mechanism.

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