I confirmed mine does not have the same communication issue as the scanner tool I just bought connects fine. But I confirmed only 2 of the monitors are ready (Fuel and Comprehensive Components Monitor)... so I guess the fun game of running through the drive cycles start. Timing is everything as my battery totally died over the winter coupled with a recent tune update, both of which I am sure contributed. And of course I am on the 2 year cycle for needing the emissions. I also confirmed both the custom and stock tune have the same strategy, but not sure why the emission system indicated a communication failure??
Not sure if this is unique to my car, but the process to confirm the emission system is ready per the manual indicates my car is ready. Turn the key to on and wait 15 seconds... if the check engine light flashes 8 times, your car is not ready... but if stays on solid, the car is ready. Mine stays on solid no matter how long I wait.