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Not all workers called utils.default_flagfile, and nova-manage explicitly said to use the one in /etc/nova/nova-manage.conf. This made development awkward since everything but nova-manage would use defaults for everything, but nova-manage would use whatever config was in /etc/nova/nova-manage.conf which was likely put there by a package of some sort.
The Choose Your Own Adventure README for Nova: You have come across a cloud computing fabric controller. It has identified itself as "Nova." It is apparent that it maintains compatability with the popular Amazon EC2 and S3 APIs. To monitor it from a distance: follow @novacc on twitter To tame it for use in your own cloud: read http://nova.openstack.org/getting.started.html To study its anatomy: read http://nova.openstack.org/architecture.html To disect it in detail: visit http://code.launchpad.net/nova To taunt it with its weaknesses: use http://bugs.launchpad.net/nova To watch it: http://hudson.openstack.org To hack at it: read HACKING To laugh at its PEP8 problems: http://hudson.openstack.org/job/nova-pep8/violations To cry over its pylint problems: http://hudson.openstack.org/job/nova-pylint/violations