You'll need to tell Alfresco whether to use uid or cn in ldap-authentication.properties. I think it defaults to uid. So if your ldap server has your username stored as a cn rather than a uid, then you'll need to change any occurance to cn. So instead of something like uid=%s,ou=people,ou=domain,o=something it would be cn=%s,ou=people,ou=domain,o=something. That way its passing whatever you type in the login box as a cn instead of a uid.
Hope that makes sense.