I understand that you changed the button rubber, which is the same that comes with triangle, circle, and square. But try taking a look at the rubber pad that presses the conductive film's connector. It has happened to me some times that this rubber doesn't press correctly and it only affects one or two buttons. The theory is that whenever you press X or other buttons, you move the film just enough to lose connection, causing you to lose the signal for the next times you press.