Application is enabled at the container level, but is not enabled for a user

Application definition settings are not flowing down to the users.
SSO preferences are not inherited

Unless the preference for "container settings to override user settings" has been set to Yes (it is No by default), user specific settings override container settings. To ensure the user always receives the settings on the container, DO NOT make any user specific settings at the user level.  Once a user specific setting has been made, it will always take precedence unless explicitly told not to.