The problem was the pump on the inlet side of the boiler would kick on whenever any zone called for heat. The pressure was enough to send hot water through each zone even if though there was only a call for heat from one zone. He told me it always worked this way and the upstairs was miserably hot.
To me it seemed as though the 3 pumps and flo-control valves were a botched add-on to zone the house.
I went over on Sunday and disconnected the pump on the inlet side of the boiler and ran each zone separately. The system worked fine, only got hot water in the zone that was calling, boiler reached temp and shut down then restarted when it cooled off again. I verified that each zone worked properly.
I'm going to leave the pump in place for a few weeks just in case a problem comes up but everything seems OK. There is a little bit of hot water creeping up the return side of a non-calling zone but it shouldn't be a problem. The original threads can be read here if you are interested.