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.