This is a problem that happens only when the device is no longer being detected by your computer. So it happens only if you actually unplug it from usb. If you have a wireless controller with usb receiver, as long as the device doesn't power off, you won't have this issue. The driver you linked just keeps the device from powering off so it's always detected.

I'm using a wired usb controller though, so if it gets unplugged it's no longer detected. The problem is FFXIV client can not detect new hardware while the client is running. Even if windows detects the new device, FFXIV client won't recognize it until you reboot the client.