Django Makemigrations not working in version 1.10 after adding new table
You could try:

Deleted everything in the django-migrations table.
Deleted all files in migrations folder and then run python manage.py makemigrations followed by python manage.py migrate as you said.

If this doesn't work, try:

Deleted everything in the django-migrations table.
Deleted all files in migrations folder, use your old model.py to run python manage.py makemigrations followed by python manage.py migrate.
Add new model, run python manage.py makemigrations followed by python manage.py migrate again.
I added some table models in models.py for the first time running the app and then ran python manage.py makemigrations followed by python manage.py migrate. This works well but after adding two more tables it doesn't work again. 
It created migrations for the changes made but when I run python manage.py migrate nothing happens. My new tables are not added to the database.
Things I have done:

Deleted all files in migrations folder and then run python manage.py makemigrationsfollowed by python manage.py migrate but the new tables are not still not getting added to the database even though the new table models show in the migration that was created i.e 0001_initial.py.
Deleted the database followed by the steps in 1 above but it still didn't solve my problem. Only the first set of tables get created.
Tried python manage.py makemigrations app_name but it still didn't help.