Found a post from a year ago where somebody offered good feedback.
http://forum.square-enix.com/ffxiv/t...=1#post1973613

Quote Originally Posted by nexen
The real problem... (hopefully SE reads)
I think FFXIV has a device enumerator such that every time a device is connected it triggers the controller code to see if FFXIV has to change controllers. Somewhere in that code, it stops responding to the currently connected controller while it determines if it has to switch controllers. Not sure how to log a bug, but being familiar with how software is built, I am fairly sure this is what is "truly" happening.