I've gone through a couple PSone controllers doing this. I'm hooking up tactile swtches for each button and I'm conneting them directly to the controller's circuit board. It always works fine for a while. By the time I get all my connections soldered, it starts acting weird. Usually it just won't work but ocationally a button press will register..
If I strip all the connections off and start over the problem remains. I just have to break open a new controller when this happens. The only difference between my set up and the way they come is *I think* the controller circuit board introduces a bit of resistance for each button. Could the absence of that resistance be ruining the controller over time?