Hi folks,
Thanks for all the advice and welcome. I did, ironically solve this problem shortly after posting this. I down graded to the public release of Mix Control and changed Logic's preference to use MTC syncing (If you would like to to do that, it is control click on the control bar to customise and check "sync". Once this is on the control bar make sure it is highlighted, turning blue) I did these both at the same time though so I can't tell which one worked. I noticed the sync was changing back to internal on Mix Control when I opened Logic so I would guess it was changing the settings. Just glad to have it sorted
The good thing to come from this is changing my power settings to optimise for audio processing, which otherwise I probably wouldn't have done. The only issue I can't solve is the huge dropouts randomly through the speakers. I sense that will be something I need to take up with Focusrite again. The sounds don't ever go onto recordings, just can be quite a shock if you're not expecting it at 9 at night after your 7th coffee
Thanks again folks.