I have spent several hours on this with no mention of setting it up in any help file or forum post so I will share my findings here in hopes of saving someone else that time.
Active Directory Logon Setup.
1. You need to make sure that the "service" for VisualCron is running as a domain user or as a user who can access active directory. By default the service runs as 'SYSTEM' which cannot access active directory thus cannot authenticate the clients that are loggin in. In other systems that use AD, there is usually an option to specify a username/password and the service uses that for AD but thats not the case in VisualCron.
2. When you go to [Settings] -> [Users/Logons] and check the box for 'Allow Active Directory Logo', there is an icon there to pull up the departments (for filter). You need to make sure that the windows user that is logged on the windows machine that is running the VisualCron client is a DOMAIN USER. It would be nice if all the requests for Active Directory queries made from client go through the server which is already able to access Active Directory but that is not the case.
Also, under [Settings] -> [Users/Logons], 'AD Server' is just the name or ip address of the Domain server. I was attempting to put in a connection string in there consisting of a domain username/password since there was no other place to put a username/password that will be used to connect to Active Directory (#1 above does this).
3. In the client before you log in.. you need to edit the server connection and select 'Use Active Directory Logon' instead of 'Use Internal Logon' (which is selected by default). If you specify your Active Directory credential and the default is still 'Use internal Logon', it will not work and you can't connect.
Hopefully this helps someone!