That is such a peculiar issue, and it's hard to even pinpoint a search result related to it in Google.

First thing you want to do is check for any recent changes in your PC, try to remember any new software you installed or updated, also type "event viewer" in the start menu search and look at the list of recent changes.

Although when you mention you even ran a system restore, that almost throws that suggestion out the window.

Do a few more hardware related tests. Unplug keyboard (keep it unplugged) and use the mouse to switch back focus, repeat with the mouse unplugged this time (and again with controller, if you use one).

One last (FFXIV related) suggestion is go to "My Documents > My Games > FINAL FANTASY XIV - A Realm Reborn" and copy the contents of that folder somewhere else (don't delete, you'll put them back after another test).

If the issue is specifically FFXIV related, you might have to reinstall it (might as well do that if you have a fast connection to download the updates quickly).

Good luck :x