On the nights it doesn't wake... did you use the car the day before?
I have "schedule departure" set for 730a, with pre-conditioning set to only occur on weekdays. This past sat night, I got home around 11:30p, plugged in the car. It charged sun morning before 6am as usual.... however I did not drive the car or unplug it at all on Sun and Monday morning, it did not pre-condition the car for my 730a departure.