Django tests broken when I have two database in settings

I have a Django (1.9.2) application with two databases (Postgres) in the settings.

And I have migrations with migrations.RunPython.

When I try to run the tests (manage.py test), migrations run twice breaking the tests. On the second execution, the database already updated to the latest version and the code called on the RunPython raise an exception.

Someone have some tip to solve this?

Thanks