Thanks for the reply Matt,
Yes all sensor calibrations are done carefully, especially compassMot as I have a jig for these that enables me to tie them down securely.
I did not expect the internal Pixhawk compass to give me sterling service as it is wedged above the PD, about 2cm sitting on a CF sheet, and below the battery, 3cm w/battery sitting on CF sheet.
The point of the test was to remove everything but the essentials and test fly.
As it was I was expecting bad toilet bowling and was poised on the trigger to catch it, I just needed to check it would fly and go into loiter, which it refused to.
No, I am not that Mike Boland (with a d) 
More test results to follow.