Have you modified your firewall to allow connections over this port? It does seem to me that License Manager is respecting the port setting.

Using the format domaincontroller:port I was able to connect to a domain controller on port 3269, which is an alternate port than the ones usually used by License Manager (389 or 636), though still on the list of defaults for domain controllers.  

A good way to troubleshoot domain controller connections is to use a very simple client, like LDP.exe, to see if you can make a connection from the same machine where License Manager is installed using the same settings. (LDP is a Windows tool included in the support tools from Windows 2003. You can  download the .cab file and find ldp.exe)