I have been dealing with this same problem for 4 days, I just solved it last night. I spent so much time redownloading the game, uninstalling programs I thought might be the problem, and even went as far as reformatting my computer and nothing worked the problem persisted . I looked up the issue everyone suggested a wireless controller or keypad to be the conflicting but I dont use either of those items. I had a USB extender plugged into the front of my computer to give me more USB slots which I had my wireless headset dongle plugged into, as it turns out the USB extender went bad causing my headset dongle to malfunction making my game stutter. It was only FFXIV that would stutter I had no issues with any other games I play. After I unplugged the USB extender and plugged my headset dongle directly into my computer I have no more problems.