An update:
I think my guess was correct. The Amixer output was way high creating distortion. There’s a Github post here https://github.com/pimusicbox/pimusicbox/pull/309/files in which jcass77 suggests changes for the file /opt/musicbox/setsound.sh. It was this file which was resetting the volume level on the Amixer on each reboot. I’ve set the DAC+ line 128 to VOLUME=70 and this is producing sound with no distortion.
Despite being told by the folks at HiFIBerry that these settings are wrong, Bram_Maes posted these Attached New HiFiBerry Dac+ but now MusicBox.local stopped working! which work as far as being able to use the musicbox.local interface - which doesn’t work if you start changing things.
Having been given a RPI2b and having lost my old 30 pin Ipod, I thought this might be a good project, but I feel the sound I had from the Ipod / Pure i-20 Dac was far superior.