I've followed the instructions (using an existing install of zimbra) for setting up samba against the LDAP of zimbra.

While the "getent" command fails to give me an expected result of showing me the new users created via zimbra, connecting via the samba protocol to the server from another ubuntu machine does work (i've tested by checking each users home folder works IE smb://{server_name}/{username})

but one oddity is that when i try to log into the ubuntu server i'm now asked for my password twice.
When trying to do anything that requires root access (IE gksudo or sudo commands) i'm also asked for my password twice. while this isn't an issue in a terminal window (IE sudo) gksudo wont display the second prompt for a password, hense all admin programs no longer work.

Does anyone have any thought on why this might be happening?

I'm guessing it's something to do with the /etc/pam.d/ config file changes.