After a few years running windows as roots seems to break. After a total of six years interacting with windows through the mouse is spotty at best. Your keyboard is bound to windows beneath the current window. Pretty much everything breaks, and you have to restart Cinnamon whenever you want to interact with a new window.
Going to try restoring from a backup from a few days prior to this. Hopefully, that fixes everything, and does not break again in two days.