That was a good idea but unfortunately it still hasn't gotten rid of the stutter. At this point I really don't have any ideas as to what else it could be. It seems like a connection problem with Square's servers since everything works fine otherwise.
I seem to recall this being caused by having the gamepad enabled in FFXIConfig but not having one plugged in. Or something like that, it's been a while. Also if you have any extraneous USB devices plugged in, try unplugging them.