I've been digging around and found it was actually some code in my .emacs file causing this not to work (although it used to previously).
The code was to automatically push/pull orgmode updates. I have since commented out the section that seemed to conflict, although I'm not sure why at the moment.
As you'll see, I haz copy and paste... :-) I'm no elisp guru, although now that I have a little problem, it's good motivation to learn.