I've noticed every time I deactivate my factory alarm and open my driver door I can hear the windows adjusting or opening a crack. They always close back up, but is this normal for entry into the car?

 

Yes that's normal. It's called indexing. Every time you open a door (driver and passenger) the window will open a tiny bit and then close back up when the door is shut. Only cars that don't have full frame doors (such as Minis) have this feature in order to prevent damage to the glass.