Onisake, looks like you've got the right perspective on this one. This effect may even been exacerbated by the system already having CPU speed modification software already (pre-)installed on it (over-clocking, tuning, etc.). If you press Ctrl+Alt+Esc you can pull up the task manager and view the processes tab. In this menu you can modify the core that the application is running on and even set its priority. By running Skype you are essentially jerry-rigging this process, forcing FINAL FANTASY XIV to run on a certain part of your CPU and it seems to be optimizing it.