I've noticed this happens as well. Usually after about an hour of play on both my Intel based laptop and AMD based desktop.
Noticeable frame skips and lagging of notes during game play. Only thing that fixes it is shutting the game down and restarting... which isn't too bad so long as you leave the aqua/minime process running.
Temps usually look well within range too, but I'll try to get a proper log of everything to see if something is spiking or looking weird.
Use the chusanhook and inject files from the segatools-chusan zip. That will fix the 6401 error.
segatools-chusan.7z