I maintain the fact that it's not a bug. It's simply a short-sighting in features - along the same line as Auto Attack and the lack thereof. There are many games that cannot interface with a gamepad properly. While support for one may be available; the game still only loads peripherals only once and that's at boot-up. Other than that, the game must be coded to search for and intercept new hardware so long as that hardware is recognized by the game on an individual level. For example; in DDO, the Xbox 360 controller only associated with the game once at start-up until enough players demanded that it's logic be added to the game's peripherals awareness. It wasn't until Module 8 that they added not only the Xbox controller, but playstation 3, madcats, logitech and many other companies that design PnP game controllers. DDO will also recognize any USB headset I connect, however, it won't recognize my Bluetooth if I pair it after the game has launched. Again; it's on an individual device level. FFXIV may already have logic for many USB PnP controllers. However, the importance of the fact that someone may disconnect that controller, then reconnect it later while the game is running, is a case few and far between. Odds are we won't see a logic for controllers until after the PS3 launch which has been postponed for God knows how long.

All of that, though, begs a question. First, a statement. I found the switchy that makes the keyboard "Chat Only".
Now - if they have that feature implemented - which screams "We know you use other things besides a keyboard", why the hell is there no controller logic? On top of that. Why is key-mapping limited to a sub-exe that cannot be run parallel with the game. Mapping keys would be great in-game for the controller!
And while I'm on this rant, Square, while I'm using a controller I cannot 'Execute' Battle Regime. I can put myself into Regime but I cannot set it off. If you'd like some information on that; BR via the controller mapping "FFXIVconfig.exe" is associated with the "Emote List" mapping. That will allow me to begin the BR and stack me action, but pressing it again does not execute the BR after all players have stacked. Please remedy this when you get around to the game controller fiasco.