Can you tell us how you use the pins.
We need to know exactly which pins you are using.
Arduino Leonardo: http://arduino.cc/en/Main/arduinoBoardLeonardo
The analog input no longer working makes no sense.
Do you use a lot of ram ?
Or do you use an analog input that is capable of PWM output ?
My best guess is, that you use a lot of ram (buffers, arrays, strings, variables), and have a stack/ram overflow.