I don't understand why the thermostat has no Y connection. I don't think this is causing the problem, but it may be a an issue when you us the AC. If R and Rc are connected to the same transformer then you could have left the jumper in place and use one wire. Try disconnecting the black from Rc and putting in the jumper. Electrically is should not matter but this extra wire may be introducing some intermittent problem. If that does not work then repeat using the black wire and removing the red. Do you have a voltmeter? Measure the voltage between R/Rc and C and see if you have 24 volts. Do this when this furnace is off and if you can when the furnace is running. You may be experiencing a voltage drop which could be causing the issue. Perhaps the thermostat is detecting this as a power failure which may cause a reset condition.

I climb up the attic open the door at furnace and find out there is a transformer that step down 120 v to 24 v . and two terminals at the second end (24v) red terminal is power 24v and the other terminal is use to connect to frame or chassis and serve as common ground so a c wire is any unused wire you can pick any color you want in the same bundle that goes from the furnace to the thermostat in my case those extra wires are trim flush to the bundle jacket on both end so I need to peel that jacket off about 2 inches on both end and connect a single wire about 2 foot long from the frame to the wire you selected (let say black) on the furnace end then the black wire on the thermostat end will be "C" wire and connect it to the "C" terminal on the new wifi fancy Honeywell or Nest. If I say anything wrong please correct me. I will do this at some other time. for now I just thinking. I signed up for smart (something) at gapower.com and they will sent me a nest gen.3 for free. I think this nest also will need "C" wire. I wait till I get the Nest then I will install both the Nest and the Honeywell at same time I will put the Nest down stair and Honeywell up stair.

Update on my original post. I did buy the thermostat from Lowes which is part of their home automation system called Iris. I originally liked it, although to get all the advantages I had to get their service at $10/month. I could track my temperature usage using my iPhone or my desktop computer. Then, about a year later, they discontinued the model of hub and sent me a new one (for free). I am very dissatisfied with the new service, it won't work with the desktop computer. But, most of all, their service is very poor. When I call, it may take an hour or more on hold before I get someone, and the most that person will give me is "I don't know". Before I switched hubs, I needed another WiFi thermostat for my new vacation home, so I got another Iris one, this time with the same, lame hub. Same problems and, in addition, the thermostat itself failed with no compensation from Lowes. The heating installer recommended a Honeywell 9000 series, which he got and installed. It works very well, so when I needed another Tstat for another zone, I got another and installed it myself (the box says "Pro", but I had no problem). Honeywell has a nice free service (mytotalconnectcomfort) which keeps track of my heating and if the tstat fails to connect, I get periodic messages telling me so (usually this is caused by either a router/cable-supplied internet failure or a power failure). I'm thinking about replacing my Iris tstat at my primary residence with the same model Honeywell, just to get the peace of mind of knowing that it's working. The 9000 series Honeywell cost $215, but they have many look-alikes at Home Depot and Lowes for about half that price, and I don't know what the difference is. I would like to have this new one on the same Honeywell as the ones I already have. Any input here?

I am not an expert the wiring used on old boilers with zoning. The circuits are simple so it just a matter of understanding the configuration. It sounds like you have three thermostats each connected to a relay. One relay is different than the other two. The three relays control three independent zone valves. The relays are needed since the values use 120V for operation. How are the relays wired to the boiler and circulator pump? Are there 24V outputs wired in parallel? Now back to your original problem. Are you planning to install a WiFi thermostat on one zone? If so, then I think you are better buying a relay that has a C (ground) wire output rather than switching relays. Another method is to wire a second 24V transformer to the thermostat. There are some YouTube videos showing how it is done. The problem with this method is the the relay and the second transformer must be wired to the same phase of the 120V line voltage. If the are are out of phase then a lot of current will flow through the transformers. They neglect to mention this in the videos.