They played a couple of recreated samples on NPR. One sounded roughly pentatonic to me; the other sounded... of indeterminate scale and/or out of tune. It's hard to say exactly how it would have sounded, because the flute allows a lot of room for bending the pitch based on things like embouchure and whatnot (I'm a former flutist).
msluyter, do you know what flutes (and other wind instruments) are generally tuned to these days? I noticed some of my sister's clarinet music books show different fingerings for sharps and flats so presumably an extended meantone? Ta :-)
Modern flutes are all in C. Not sure what you mean by "extended meantone." Most wind instruments can have slightly different fingerings for the same note (more prevalent in clarinet than flute, actually). These may have slightly different intonation/sound. Perhaps that's what you're seeing?
Check it out for yourself:
http://www.npr.org/templates/story/story.php?storyId=1058231...