I think I have worked it out.
My Mbox 3 is screwed. It has troubles with any previous sessions I have created using 48k or if I create a new session using 48k.
But If I create a new session using 44.1k it's fine.
I saw a thread regarding if you use the tuner and it report a different note to what you are playing. I.E. you play and "E" and it reports it as halfway between F and F#.... if that makes sense?
http://www.gearslutz.com/board/music...ple-rates.html