Kev,
I think that you could be onto something re the alignment of the disc - I will check out my semi-floater to see - but it was the original disc off of the bike, and I know the spindle bush was located properly cos I have fallen for that one before!
However, I did not have any problems fitting new pads to either disc setup - which I have experienced when the disc and caliper are not aligned properly. Also I have run identical full-floaters and calipers on my 851 on both road and track without any noticeable problems............
I will pop the pistons out of the caliper tonight and see what the inside is like.
Maybe we were just using our brakes too much for a single disc setup?