I have been having the exact same problems and after so much troubleshooting I realised FFXIV is the only game I am having issues with. It's so frustrating because it's actively discouraging me from playing the game. Every time I load up I wonder if my controller will actually work. I know the exact pattern as well for this issue... that's how many times it's been happening to me. Edit: also makes me sad because I got the 8bitdo ultimate controller for my bday specifically because I love playing FFXIV on controller.