The controller support came with 3.4 but that was for Dualshock 4 only. I use a ds4 and have zero issues, if you both started getting the issue after that patch then it might be to do with the game and is out of your hands. I find it odd that a 360 controller has the same issues when its compatible with windows. Do you get the same issues with other games on any controller or is it specificly FFXIV?

If its just FFXIV perhaps you could borrow a ds4 to try out?