OK, so I am not sure that I follow exactly what you did, but it does appear that you have essentially proven that the problem follows zones to whatever channel you connect them too. (Correct me if you disagree) Due to that, I can’t personally think of a way that the flowmeter or system itself could be faulty*. *More on this later.
It would appear that these fluctuations actually exist in your system. So, I heard through various industry contacts that Rachio has sold many many 1000s of these meters. There are less than 30 questions posted in 2019 in WFM category and virtually none have been failures, but there is a handful of people who do seem to have a problem with fluctuation of flow. One poster claimed that a certain type of sprinkler head is “not compatible” with the flowmeter and they changed out the heads and that made the flow be consistent and everything worked. I am not sure that I believe that…I tend to believe they had a problem that was fixed during the replacement of heads. I mainly believe this based on the obviously small fraction of a percentage of people who have this problem. Or is this type of head very rare?
Your situation is different in that your system worked for some period of time before the problem cropped up. The question is what types of things can cause this?
QUESTION TO PROS: Is there a type of sprinkler head that doesn’t flow consistently? Could a fluttering valve (partially open) or obstruction cause this? How about a leak?
*Olliesshop, the problem that crops up for you and an apparent tiny fraction of others is the decision to make the meter wireless and just do a sample shortly after turn on to save power. (a reasonable tradeoff) This is a perfectly defensible way to design the meter to save wiring though not my preference. If you could monitor in real time by wires, fluctuations could be factored in and accounted for.
This probably ends my ability to help you. I’d say your choice would be find the problem causing these fluctuations in flow or don’t set lower limits for flow on those zones and only worry about high limits. (which are more important since they indicate a leak) I suppose you could extend your pressurization time to the maximum and see if that helps.
I hope that someone who knows sprinkler components more intimately will eventually chime in about a possible source(s) of these erratic flows.