Cross over heat transfer

Check valves are in the pump, or you could have separate flow check valves. Pictures may help

flow checks stop forward flow unless the circulator for that zone is running.

Spring checks used in hydronics have a spring with a 1/2 psi "pop" opening. Weak enough for even a small circ to push open.

That is enough to prevent gravity or ghost flow induced by the buoyancy difference between hot and cold fluid. Which is the concept the the old gravity systems operated under.

Older style cast iron flo checks had a tapered weight inside that acted as the spring does,

A couple of questions.

Why are you regulating flow with ball valves? Why not use balancing valves made for that purpose? The flow thru 3/4" copper pipe should be about 4 GPM max. Ball valves must be 90%+ closed before regulating.

Why are some of the ball valves fully open on Zone 3 and partially open on one 1 &2?

Is it possible that Zone 3 mixing valve is installed backward (H to C or C to H)? Mixing valves are directional and there must be a temperature differential between the H & C inputs for it to function properly.

The EX-tank should have been installed on the supply instead of the return to the boiler. There is more efficient air removal in that position and pumps run better being on the output of the EX-tank.

Your diagram shows a good chance for ghost flows because of a lack of check valves on the returns from the heating loops.

I don't see a need of a gravity flow check in that position. I would put one in the volute of the boiler pump, tho.

Is it possible that both pumps run when Zone 2 is running?

I would close the ball valve going to the mixing valve on Zone 3 and run Zone 2 and see if Zone 3 still over heats. Tell us what happens.

"Check valves would stop reverse flow on the pump feed side, but how do you stop flow coming from return side back into the mix valve and thru the pump in the correct flow direction?" You put check valves on the return side, too.

"Is it better to zone with zone valve rather than circulators?" Zone valves give positive shut off where as circulators may not stop flow thru the volute if a pressure differential exists between the input and output of the volute.

it needs to be repiped or heavily modified to work properly. I would not spend time and money on questionable work arounds

Take a pic from aways back, maybe we can see where modifications could be made without starting over

Although sawzall surgery is sometimes the only way forward

The sketch a couple posts up is about as simple as you can make it

A boiler loop and 6 sets of tees

Yes, globe valves are more preferable than ball valves, but they don't tell you anything. What you want to know is the flow thru the piping of a sub system. That's what balancing valves do. You have a "HEATING SYSTEM" as your diagram shows, but, it is comprised of many sub systems. Zone 1, 2, & 3 are sub systems. You don't want one sub sys interfering with another sub sys, which is your problem. That's what closely spaced tees and hydrolic separators do. They prevent interference between sub sys.

It's all about flows of heated water and controlling those flows, sending it where you want it to go and stopping it from going where you don't want it to go. There are tons of Caleffi videos that show you how to achieve this goal.

But, We often want a quick fix. So, based upon your diagram, I would put a inline balancing valves on the returns of each zone to the common return pipe, such as the Caleffi Quicksetter Balancing Valve w/Flow Meter. But, they're pricey, so I would do it on Zone 2 and a Caleffi inline check valve on the return from Zone 3 if you have ghost flows up the return from Zone 2. It's difficult to know the fix unless you know the cause.

I agree, correct piping is the solution. I'm cheap, so I look for an economical solution that might work. Water flowing under its own head takes the path of least resistance, But, water under pressure can do all kinds of untoward things, I would think. Given the choice of two paths, under pressure, most water will flow thru the least resistive path.

Perhaps, a Taco 3way i-series mixing valve could be configured to work on Zone 3. I have no idea where the flow of hot water is getting into Zone 3, however, one can be sure it is thru, either, the supply or return or both?.

I'm really a big believer in balancing valves to regulate flow in an over pumped zone. Not saying it is, but, I don't know.

Just spit-balling here. What about a pressure differential valve at the end of the supply manifold piping to the return manifold piping. The boiler pump is additive to the zone pumps as the pressure loss thru the cast iron boiler is low and the supply piping pressure loss may be low, too. We use to do that with zone valves before variable speed pumps.

Wfrcrownbwf, asked, "Also finding it interesting that these layouts with " closely spaced tees" are putting the return back into the supply line??? Won't that dilute the supply heat to the next zone?" Yes, definitely. But, you notice there's always a but, not all zones do run at the same time, also, the flow in GPMs in the common piping is higher than the flow thru the zones. That's a mitigating factor.

I know your sys isn't perfect as it has mistakes in its construction, but, there we go again, the problem is that when Zone 2 is running whether Zone 3 is running or not, Zone 3 over heats. This can only happen thru the common piping supply and or return. If the sys is satisfactory in your opinion except for this problem, then fix the problem. You have many choices some more costly than others. There are a lot of options, maybe call in a hydronic expert to give you hands on testing and advice and there are options by the fearless pros on this site.

Have you considered that you might have a faulty mixing valve on Zone 3. That's where temperature checks would be helpful.

hot_rod, when I said, "water flowing under its own head…", I meant an open sys. That came from a paper that I read a jillion years ago, written by a plumbing or sanitary engineer discussing flows in a sewer pipe. That was his sentence and I liked it.

I know how head is used in hydronics, mechanical energy (pump) applied to water causing it to flow. When you read my replies, I always say "Head Energy". Water flowing under its own head is exactly the same thing in an open sys, energy imparted to water causing it to flow. What is the magical motor that imparts energy to water that causes it to flow in an open sys? It's called Gravity. Who ever thought up Gravity sure knew what he was doing. We couldn't live {exist) without Gravity. So, I think, open and closed head energy is about the same.