If the client says it's communication successfully but ePO says it isn't then i suspect that you might have duplicate machine entries within your system tree (or 2 ePO servers).
I.e. the clients are reporting correctly but to an entry in a different folder in the system tree.
What is the circumstances of these 'rogue' machines? Are they laptops, pc's or virtual machines at the other end of a VPN/VLAN/WAN Subnet? or are they plain old normal PC's on your LAN?
Also have these machines been installed via an hardrive image?
Well thats the part I dont get because I have one server, no duplicate lists or entries. The devices are all laptops, a variety of makes and models, no real pattern as if to say 'only toshiba' or something. Most are seperate VLANs than the one the server is on, and they can all ping back just fine from either end. None are done via image, and I just noticed on one of the logs this is a common Warning:
2012-02-01 12:43:11,562 WARNING MfeEpeServiceLPCServer LPC state initialized, but runtime unavailable. Please check MA installation.
2012-02-01 13:21:12,250 WARNING MfeEpeEsEncryptionInformationService ..\..\..\Src\EpeFsmHostErrorHandler.cpp: EPE_fsm_host_error_handler::handle: 71: Received service unavailable exception: The service MfeEpeEncryptionInformationServiceClient is currently unavailable
I am going to install EE GO and test the communication between to see if that will identify any issues.