I know this is an old question but I fought with this same issue all day and my solution was a simple one.
I had my directory structure something along the lines of...
apps/
   app/
      __init__.py
      app_sub1/
           __init__.py
           models.py
      app_sub2/
           __init__.py
           models.py
      app_sub3/
           __init__.py
           models.py
   app2/
      __init__.py
      app2_sub1/
           __init__.py
           models.py
      app2_sub2/
           __init__.py
           models.py
      app2_sub3/
           __init__.py
           models.py
    main_app/
      __init__.py
      models.py
And since all the other models up until the one I had a problem with were being imported somewhere else that ended up importing from main_app which was registered in the INSTALLED_APPS, I just got lucky that they all worked.
But since I only added each app to INSTALLED_APPS and not the app_sub* when I finally added a new models file that wasn't imported ANYWHERE else, Django totally ignored it. 
My fix was adding a models.py file to the base directory of each app like this... 
apps/
   app/
      __init__.py
      models.py <<<<<<<<<<--------------------------
      app_sub1/
           __init__.py
           models.py
      app_sub2/
           __init__.py
           models.py
      app_sub3/
           __init__.py
           models.py
   app2/
      __init__.py
      models.py <<<<<<<<<<--------------------------
      app2_sub1/
           __init__.py
           models.py
      app2_sub2/
           __init__.py
           models.py
      app2_sub3/
           __init__.py
           models.py
    main_app/
      __init__.py
      models.py
and then add from apps.app.app_sub1 import * and so on to each of the app level models.py files.
Bleh... this took me SO long to figure out and I couldn't find the solution anywhere... I even went to page 2 of the google results.
Hope this helps someone!