I've been having controller issues too lately. I use my Ps4 remote to play the game and it's starting to boil to a head that the port of this game was half assed. I love this game and love to play it, but if my controller gets unplugged mid game and never reconnects to Pso2, then there's som'in wrong with the game. I have to restart the entire pc, I repeat, the whole pc to fix the controller not reading issue. This is beyond ridiculous. They better have some fixes in this coming update, cause this is madness.
edit: Just logging out of Windows worked, saving me a ton of time. Pso2 seems to lock a driver or som'in and won't let go when it denies a controller connection. So it's not our fault, specially if the controller works in other games.