Hi
If you are getting a no response for the standard domain query (source ip with MSM) indicate that you have the netbios name configured incorrectly on the controller Active Directory section.
You can also do a simple trace on the controller itself (Tools --> Network Trace --> select either Accessport or Internet port depending upon which is the next hop to reach the DNS server ip). You can filter for port 53 or 389 (filter command: port 53 or port 389). This should give you the whole transaction starting from DNS query and LDAP binding.