2) when I test login to qlikview it shows me all the data and ignores the section access
If testing on the desktop client and switching between users, you will need to fully exit QlikView to be able to change user, as the user details are retained if you just reload the same application.
3) when I try to refresh the data on the server side it fails to reload and I receive an error saying it cannot access
The service account that is running the QlikView Distribution Service, must be listed in the Secvtion Access script as an admin user with full access to all data. Otherwise section access will only load data that the service account login has access to, and data will be missing for other users.
This may also cause the missing data you are seeing in Q1 when I test login to qlikview it only shows the department Name as a selection op[tion but NO data associated to that department