If you are on a site that runs downhill towards the back of the rig, the first step of auto level, lowering the rig in the front, will stop the whole process if the jacks bottom out. (Found that out from a couple way off level sites). If that is the case, then what you are doing (manually raising the front, then manually operating the sides) is about all you can do.
On the other hand, if the fronts always fully retract and then stop, then the unit may need to be re-calibrated. As I remember, you manually level the rig to your desired level. Turn off the unit. Press the down button 10 times, then the up button 10 times. The unit should then wake up and ask you to press Enter to verify that you want to reset the level to that position.