This is really PyDev's problem with Django 1.4. A new release (2.5.0) will be released later this week, properly supporting layout changes in Django 1.4.
You can still use the project created in this way, but you need to do some manual things:
Move the contents inside the folder created in your module (it was a structural change made in django 1.4)
Settings.py parameters will not contain information that you entered in the wizard (for example: manually edit settings.py)
In the django project properties (right click on the project> properties and check the django properties page), you must set the correct settings in the settings module and manage.py.
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