Implementing a login page with Flask
Flask-Login is a very basic login manager that is built upon with a few other user management frameworks. I have been using Flask-User in production for over 1.5 years with about 30K users and have not had any problems with it (which uses flask-login under the hood). The maintainer is active and has responded to my issues in a timely manner.
It handles user login, registration, lost password, and even email confirmations if so desired. It comes with some pre-built forms if you don't want to mess with that but is easily customizable if you do.
Sounds like maybe when login_user gets called the login is not being persisted. I would make sure however you're doing your sessions is actually storing the login.