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.
That's not what he said. He has analogWrites() (PWM outputs) stop working when he uses the tone library.
Bottom line, AnalogWrite commands use timer resources to support the pwm output pins. The ton library uses timers depending on how many simultaneous notes you wish to use. So there can be a conflict for timer resources, so careful selection of pin numbers used and a understanding of the timer resources available is the key to allowing both functionalities to exist in the same sketch. Different atmega chips have different number of timers so that is also a variable to consider.