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After a few days of struggling with this problem I finally found the solution, and the real origin of this problem.
First of all I’ve been using Django 1.6.10. In both applications I have registered handlers for user_logged_in signals. I put the proper functions and bindings(user_logged_in.connect(handler)) into the file called signals.py in both apps. Then signals.py was imported in __init__.py, to make the signals connection work. There was also another dependance on the models.py in one of the files, which was also imported into signals.py- this was done in one of the apps. Getting to the point, the problem was circular imports in one of the app. The solution I found to work was to move signals.py contents to models.py, remove signals imports from __init__.py.