Ensure that the following box is not checked: QMC > User Directory Connectors > Edit the local connector > User Sync Settings: Fetch user data on first access, then keep in sync. This is slightly unintuitive, but it is explained in the Qlik Sense Help on this section (http://help.qlik.com/sense/2.0/en-US/online/#../Subsystems/ManagementConsole/Content/edit-user-directory-connector.htm) that if this box is checked then it will only sync users who have previously logged into the QMC / Hub.
What Levi suggested should take care of the issue. I'm guessing, if you don't see the Users under the local Server name, you probably get the users under "WORKGROUP" name (At least this is what I experienced when we started using the early QS version).
If none of the above works, could you provide a screenshot of the followings, it might be helpful to visualize what's missing:
1. 1-2 users name you have listed in the Local User List directory (if possible the exact SERVER name as well)
2. QlikSense "User Directory Connector" screen
3. QlikSense "Users" screen
4. QlikSense "Tasks" screen