Solved Issues

Digital Write:

      Digital Write is not a problem anymore. It basically does analogWrite(pin, 255).

Analog Read:

     - AnalogRead() is now returning a value in the correct range (0 - 1023)

      A12 - A15 are now returning non-inverted values

Timer:

     millis() function now returns precise values. It was faster before.

Libraries:

Servo Motor:

     This library is working and it can control a maximum of 8 servos. It uses timer TCD0 to generate the Output Compare interruption, so don’t use PD3 (D3) to generate PWM when using the Servo library.

DMX:

     Same problem, DMX library uses TCC0 as timer, so don’t try to use PD2 (D2) to generate it.

Wire(I2C):

     The Wire Library has the same behavior of Arduino’s. The only important thing to notice is that you have to read your data (Wire.read()) before calling Wire.endTransmission(true). In Arduino, it doesn’t matter.