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/arduinoBoardLeonardoThe 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.
How can we feed back this info to update the reference page for tone()?-AH-
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