I have never even heard of this issue man, if your reinstalling windows, your basically formatting your machine. There may be some driver conflict or piece of hardware that is conflicting. Or some software that you are installing after the game that is causing this.

The only way to test this is by not installing any applications other than FFXIV and see that if with just the game installed if it does the same thing. This should narrow it down for you to try to figure out exactly what is causing the conflict.