On this particular network, that I've install Zentyal, Microsoft Active Directory is managing the domain controllers.
I originally installed Zentyal 3.0 as an additional domain controller, so that it could provide jabber instant messaging in a manner where they could login with Pidgin using their domain user credentials. I couldn't get it to work at first, because I had the settings wrong in pidgin. Instead of putting the domain.lan as the domain, I was putting in zentyal.domain.lan. After removing "Zentyal", stuff started working.
Also, the additional domain controller didn't correctly replicate LDAP from Microsoft Active Directory until I upgraded to Zentyal 3.2.2.
To answer your question (to some degree), when I add a user using Microsoft Active Directory, that user gets replication to the Zentyal (because Zentyal is set as an additional domain controller). And immediately I'm able to setup pidgin for that user and it works.
You are saying that at first you set up a user with no Jabber account, and now you can't give them one?
Maybe you could try deleting that user, and then adding them back again with Jabber from the get-go?
One thing you must watch out for though is this. Remember the user you create when you installed Zentyal originally? That username is dead as far as LDAP is concerned. You can't add that username to LDAP, and therefore you can't setup chat for that username. That user name is just for logging in to the web interface and CLI. If you try to add that username as a LDAP it will fail, because there's already a /home/user folder for that username dedicated to administrative tasks.