I've been using a controller to play, but after unplugging it and plugging it back in earlier before starting PSO2 today the game suddenly won't recognize it. I'm using a Logitech F310, and it's worked before after plugging it back in on other occasions. Windows recognizes the controller and it works with other applications, so I'm not sure why it wouldn't work with PSO2.

that is probably related to the control slot that Windows uses it, when you connect a controller Windows will put it in a slot but for some games it will only work if is in the first slot, to not have to deal with that issue frequently don't connect the controller after doing login in the main user, now to fix it if you connect the controller after doing the login just do logoff of the user and login again that will reset the order of the controllers of the user