I know it is considered rude to reply to one's own post, but I thought it might stop needless replies. I have found the cause of one of the problems, slow distorted playback, it was set in control to half speed, my fault (although I hadn't set it to this!). The sound is now clear, at proper speed (and pitch, I checked against my concert pitch flute) and undistorted.
I am still amazed at the number (and relative amplitude) of the harmonics I see using the fft. Any thoughts?

The screen shot above shows a recording of a Baroque flute concerto. The fft spectrum shows a single flute note (actually its an A, an octave above middle C, confirmed on my flute) and has its fundamental at 880 Hz (by definition and by the software (well very nearly)). A flute should have just a fundamental frequency (880Hz) second harmonic (at 1760 Hz) and third and fourth, but little else, but this trace shows harmonics up to at least the tenth harmonic with relatively high amplitude. This should not be?
cheers
Waaza