How are you importing the packages under site-dependencies?
Slightly off topic to your question, but I never liked the "default" project layout for Django so I have a script that lays my projects out like so:
myproject/
apps/
vendor/
vendor/django/
config/__init__.py
config/urls.py
config/settings/
config/settings/__init__.py
config/settings/base.py
config/settings/hostname.py
templates/
media/
script/manage.py
The included manage.py is tweaked to add config, apps and vendor to python path ('myproject' itself is not in the python path) and to import config/settings/hostname.py as the settings module (where hostname would be the actual host name of the computer). Any 3rd party apps go in vendor (eg, django itself) and apps for this project go in the apps directory.
It's a bit unconventional, but I like the setup.