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Intermittent Issue: Indirect calling for heat for 1+ hrs?

Quick Overview

Maybe this is a failing thermostat? I have reason to think it's actually on for over 2 hrs. Often, if I just manually toggle the thermostat on and off, the hot water tank heats up quickly (even if it's almost completely cold; reason for that below).

This is also inconsistent; I can't figure out what causes it. I actually set up an old phone as a time-lapse camera and recorded for ~3 days and didn't catch it doing that at all.

No one is complaining about cold showers (despite the thermostat not kicking off until I turn it all the way down).

An off-on toggle of the thermostat will bring the DHW up to temp in reasonable time.

The (Janky) System:

I have Munchkin with a Triangle Tube indirect hot water tank, all controlled by Zone Valves (the installers didn't do anything right on this). I assume install date on these is the same; roughly circa 2006.

It's controlled via a Taco 3-Zone ZVC so I can actually use the ODR features of it (that's my doing, details on that below). Taco ZVC has priority set to 1 hr, after which it opens all valves that are calling for heat.

More Details

There have been multiple times where I'll go downstairs and see the Taco with all the zone valves open. So that means that it's been calling for heat for 1 hr. Last night it did it, and only 1 person had gotten a shower within the past few hrs (with a low-flow head, too. It was a tenant who is on the third floor). Heck, once it was doing it at 4am.

I have reason to believe that it's actually running for 2 hrs, though. That's because of the janky way my boiler is setup. I left the circular controls for the secondary pump unenergized and am using them as the TT call for the Munckin (link to discussion is below):

The Munckin is set to have a 60min override for the hot water tank, before it reverts to CH output temps.

My Theory

So, my understanding is things would go like this:

ZVC gets a call for DHW and CH. Sends a call for DHW to the Munckin. 1 hr later, DHW is still calling, so it opens all the valves and sends both a DHW and CH call to the boiler. Muchkin receives both calls and it's override programing starts. It sends DHW-temp water out (which is now going to the whole system (because the ZVC has both zone valuves open). After 1 hr, it reverts to CH water temps.

There have been multiple times this winter that I've gone downstairs and seen both zone valves open AND the output temp at CH levels (~90-110 degrees), leading me to believe the hot water tank has been going for >2hrs. When turning down the t-stat on the Indirect, it's basically completely "cold" (all the way off).

(why is the HW tank so cold? I don't think it's from use; one shower shouldn't run it down that far. I'm pretty sure the HW tank basically acts as a battery in this situation; the cooler CH water is run through it and the HW tank reservoir warms all that water up).

Typically, I'll just turn up the stat from there a little bit at a time (so it doesn't run for 2+ hours again while trying to heat it up). But last night I said "screw it" and turned the temperature all the way up to "normal". And it heated up in less than 2 hrs.

More Discussion on boiler setup: