(Possibly related to this question but I do not have the expertise to diagnose at the level of the author of that question)
I moved into a new house recently that was billed as having three heating zones, one per floor. The home inspection did not turn up anything unusual, though the inspector really just made sure the boiler was running and he could feel heat on one floor.
After moving in a few days ago, my wife and I had a hard time sleeping the first night or two because it was so warm in our bedroom on the third floor! After some experimenting, I have discovered that the first floor thermostat seems to make the baseboards on the third floor run in addition to the ones on the first floor. The third floor thermostat will also make the third floor baseboards run, but not the first floor ones (I think -- haven't actually verified that).
I went down in the basement to follow the piping around and it all seems correct in that I didn't see any odd runs up to other floors off of the first floor run. The only common connection point I could find was what I assume to be the return.
So, this leads me to believe there is a wiring issue with the relays and/or pumps that control zones 1 and 3. I have attached photos of both sets of equipment. The third floor is hooked up to the R847A on the left, while the first floor is hooked up to the R845A on the (far) right.
Note the brown wiring that connects all three relays to each other. I don't know why this is here (as this is my first time dealing with baseboard heat, boilers, relays, and pumps) but my suspicion is that the issue lies here somewhere.
Below are the pumps that connect the boiler output to the various baseboard runs. Again, third floor is on the left and first floor is on the (far) right.
I've noticed there is an additional box (shown in the bottom left of the photo below) that the R847A also connects to. I'm not sure of its purpose. This is my second area of suspicion.
I realize nobody may be able to fully diagnose the issue from these photos, but I'd like to see if there is an easy answer before I call in a heating system specialist.