The problem appears to be that the focus indicator was slightly off target (I only use the centre point) and the camera was focussing on the background. In my defence it was a very dark cloister in Durham Cathedral and the focus indicator was only just off target. I used the Canon EOS viewer utility to proove this, it will show the focus points used and which one was used for the focus. The other images had too low a shutter speed even for the IS system.
Thanks for your interest,
Vincent