The zones each have a separate connection for return flow, so three. It looks like the return for the zone that doesn't have the best flow isn't complete. The return doesn't run all the way to the wall with the vent on the first floor. The return is just sucking under the floor. And I guess passively pulling from the vent on the first floor.
One of the main trunks of ductwork supplying heat comes off the furnace and does two 90 degree angles runs 15 feet and the does two more 90 degree turns, to drop 10 inches, and then Ts into the ductwork which then branches at 90 degrees into the 6" branch ducts that supply the floor registers. Could this be the issue? I'm looking at the other zones and they run off at 90 degrees at one point before exiting through the registers. Is there a calculator??
As for the second floor, it turns out we have a second furnace in the attic space that heats it and was missed by our inspector. I just found it hidden in a space which I guess would be considered a third floor. Anyway that floor works great.
We purchased our house in the spring and didn't have the heat running until October. This HVAC system has had issues since we bought it. Every time I fix something I find a new / old problem that needs attention.