I would try unplugging the controller, then completely removing the drivers for it. Might we worth it to see if one of the cleaner programs can do a sweep to remove all references to the drivers. Try plugging the controller in and letting it do its thing. Then run windows update to get the latest drivers. Those drivers have given me no issues with the 360 controller. Run the config program to set up the game pad, and see if that helps.

Alternately, you can try plugging the controller into a USB port that has -never- been used for the controller (this is less likely to work however, since it will still use whichever drivers are already on the computer and if there is a problem with them, this won't fix it.)

If that does work, post your specs for the computer using the FFXIV Config tool just in case there is something there, and we'll see if there is anything we can do to help.