Yup. I feel stupid.
I had my PC flight stick plugged into a USB port when I believed it had been unplugged.
All of the lights and display were out on the stick too.
However, it was connected, and it was being read in parallel with the PS3 controller which explains the mad calibration problem.
Flying with the DS3 is good again. Flying with the X52 Flight stick is easier though.
So, PEBKAC error again. I must stop being so stupid. :-/