Originally Posted by
Xavier
When you opened the console up, did you disconnect the controller board from the console, or did you leave it connected while cleaning the pin connector? If you did disconnect it, then maybe you didn't reconnect it properly. However, if you didn't disconnect it at all, you might try doing that and leaving it disconnected for a few minutes. Sometimes disconnecting it can reset the codes in the console so that the controllers work properly again. Just make sure to discharge the system first before you do this to be most effective. To discharge the system just unplug the power adapter from the console then turn the console on. You'll see the red light flash for a split second before going back out. The system is now discharged. This is a bit of a leap in theory I admit but still a possibility.
Also, when you opened up the console, how did it look inside? Was it really dirty? Did you only clean the pin connectors or did you have to clean other things as well? Another possibility is that maybe the controller board is dirty. Might not be a bad idea to take some rubbing alcohol (at least 70%) and clean it. Worth a shot in my opinion.
Finally did you try swapping controllers? Not necessarily using a different controller, although that would be most helpful, but try switching the controller in port 1 with the controller in port 2 and vice versa to see what happens.