I have several tunable flutes and whistles. Sweet rosewoods in C and D, a Copeland D, high and low Overtons in E, a Sweet Resonance blackwood flute, and an ebony keyless from Lark In the Morning.
They all play very well in tune, as you would expect, but when I play them I need the tuning slide all the way in on every instrument. It’s never been a problem because we use guitars, mandolin, and banjo all kept at concert pitch with a pair of high quality electronic tuners. I’ve never had to play against an ‘untunable’ instrument like a concertina or accordion, so I’ve never had the need to play sharp anyway. I have no trouble at all with intonation.
It must be part of my playing style that causes this, but it’s hard to imagine playing consitently flat with so many different flutes. Every one of these is supposedly designed to play at pitch with the slide pulled out a bit. I could understand playing a flute flat because of a bad embouchure habbit, or having one of the whistles a bit flat, but all seven of them?
Like I said, I have no real problem, but what do you think causes this? Unlike a session whistler, I only play each instrument for one or two songs in a set, so they are always pretty cold. Could that be it?