So after working through an install of ePO and testing things out with multiple domains I noticed that ePO works off of netbios or perhaps just the short hostname. When I tried to ping or push an agent to an endpoint in a foreign domain I surmised that the ePO server was not using the FQDN during its communications. The remedy I found for this was adding domain suffixes to the network adapter configuration of my server.
Is this right? Does ePO seriously NOT use FQDNs?
I lost about an entire day trying to prove this isn't true but was unable. Even with all the appropriate DNS forwarders in place, registering the remote DCs, and using AD synch for various system tree folders I still was unable to ping or push an agent to an endpoint. I am Jack's utter disbelief.