I've got a small little test file with some medical gas piping in it. A have a Zone Valve Box (Oxygen, Air, Vac) on the north wall that is serving 3 wall consoles (each having Oxygen, Air, Vac) on the south wall.
On the ZVB I have 3 inlets coming in and 3 out the other side. I initially created the system with the 3 "in" connectors. Then right clicked the "out" connectors and used Add to System, clicked the ZVB family and then selected the appropriate system. I repeated this for the wall consoles (right click on connectors, Add to system).
So all the connectors seem to be on the correct system, but when I go to pipe it up I get sections that are unassigned systems (show as black).