They were, in fact, three different brands. If they’re listening to harmonics, of course, depending on what instrument it is, the harmonics will be different, so that could put things quite a lot out.
It can also indicate a problem with the instrument. That happened with my pipes. People would tune my bass drone with a tuner and it would sound out of tune, and then they’d tune by ear, and the tuner would say out of tune.
So I took my pipes to a pipemaker, and he found the wood had moved, causing the bores to go out of shape. A few minutes with a reamer and he had them straightened out (no pun intended). After that they started tuning like everyone else’s pipes – tuner and ear in agreement.
With a fiddle, it might be an indication of bad strings. Strings get uneven as they wear (thinner here, accumulations of “stuff” there), and that causes the harmonics to drift from the fundamental. Or depending on the location and sensitivity of the tuner, it might be picking up the string afterlengths.
I think tuners have their place, but they’re just a tool – like any other tool they can do more harm than good if the operator doesn’t know the proper uses and limitations. 
Well, I’m not sure what infinite breath control is. There’s normal breath control in playing any whistle or mouth-blown wind, and that’s all the Susato wants. Today I checked the 7 Susatos in various pitches and bores I have handy here against the Shaku tuner, Flutini, my Conn Strobotuner, and my ears. And none of them has any intonation problems or specifically octave intonation problems. If anything, it’s fairly easy to blow the 2nd registers sharp, though it’s also easy not to.
If yours is that far off, you might want to have Mike Kelischek take a look at it. I have found him very accommodating if there’s a technical problem. I did once have a Susato wide bore recorder with very funky intonation, which the Susato folks corrected. But every Susato whistle I’ve ever tried has been consistently spot on.
FWIW, my Mellow Dog has no intonation problems either.
That’s interesting. My Mellow Dog seems to be nearly perfectly just.
My Susato D seems to be much closer to ET (intentionally mis-tuned, by definition).
Yes, Susatos are set up for ET. Jerry’s scheme is somewhere between ET and JI, as I recall. We had discussions about this when we were developing the Blackbird.
With whistle tuning there’s always an interplay between the tuning that’s “built into” the whistle and the blowing approach of the specific player.
I’ve known a few “classical” guys over the years who have picked up playing whistle, guys with Perfect Pitch. For them, every whistle is right in tune because they automatically adjust their breath to create each note perfectly in tune, without ever thinking about it or being aware of it. That’s what they tell me, anyhow.
One guy told me he got frustrated trying to make his own PVC flute because no matter where he placed the toneholes he got the same scale. He said he was incapable of letting the flute tell HIM how it was tuned.
I’m not in that boat at all! I don’t have Perfect Pitch and I need to have a whistle that plays as close to perfect as possible on the most even breath possible, so that I can play along without too much worry and play acceptably in tune.
When I started playing whistle everyone played Generations, the only thing available except for Clark C’s, and everyone had to get used to how they were tuned.
The second octave was flat so you had to get used to underblowing the first octave and stongly blowing the second octave. In addition, perhaps as an intentional “bridge” between the sharp first octave and flat second octave, each octave got progressively flatter as you went up. I suppose the intention was to blow progressively harder, note by note, as you progressed from Bottom D to High B.
Generations of whistle players got accustomed to this tuning approach and played these whistles perfectly in tune. Still today many modern whistles are tuned like that. I think of it as “Generation tuning”. Two Overtons I recently bought, a low E and a low Eb, are tuned like this.
Other modern whistles are tuned more evenly, with each octave in tune within itself using an even breath, and the relationship between the two octaves right in tune using of course the necessary change in airstream to change octaves. Whistles tuned like this, to someone used to traditional Generation tuning, have a flat first octave and a sharp second octave and one has to get accustomed to blowing the first octave strongly and backing off on the second octave. In other words there’s very little change in airstream required to switch between octaves and stay in tune. My Burkes and MK are tuned like this.
Any tuning approach is “right” to the person who is accustomed to it!