We are running EOC 1.1 SP1 and had this issue for some time. Best way I can show it is with screenshots
Network Atlas of map. All objects show up and green.

Here is the same map on EOC. Tooltip shows up and green, but some unknowns. Objects on map also show unknown "dot".

I do have 6 "unknown" objects on the map ( 2 lines and 2 graphics ).