If I understand your problem correctly, you are having a 2nd valid interrupt occur while the first ISR is still executing? If it is not a keybounce problem is it possible that you are doing too much in the ISR? If that is the case try to shorten the ISR to the bare minimum. Use the ISR to input the keyboard data to a circular buffer, exit the ISR and let your MAIN code handle the remaining parts of your keyboard routine.

Hal