jSubbz - Not Square-Enix support, but...
  1. Do you have either your Windows wallpaper randomly cycling or Wallpaper Engine running? For whatever reason, when the wallpaper cycles it can cause a 'catch' in animation (though I wouldn't imagine you have it running so constantly that it'd cause it every 10 seconds) and Wallpaper Engine sometimes seems to get into a 'war' with certain games (including FFXIV) over who has access to graphics stuff at a particular moment (which does seem to cause a cyclical 'hiccup' in framerate with certain wallpapers).
  2. You mention running with 'many programs at once'; as Rhaervis mentions is it possible to briefly try running FFXIV with most of those other programs exited (just to see if there's a conflict between any of them and FFXIV)?