6.3.1 does things a little differently. The Directory Service Query connector is only for Directory Service Groups. To enable LDAP authentication, you'll need to look at this document:
Specifically:
- Open your Microsoft Management Console (MMC) and create at least one security group called ROLE_LEM_ADMINISTRATORS in Active Directory Users and Computers.
- Jump down to the section titled "Configure access to Active Directory on your virtual appliance" and follow steps 1 to 5
- Add the users you want to have access to the AD group(s) you created
- Log into LEM with fully.qualified.contoso.domain\username and it should work