The "brain" in the leveling system reads signals from a leveling device mounted in the underbelly to determine when the coach is level. Zero Calibration tells the "brain" to remember the current position of the leveling device and use that as the reference point for the coach being level. So to calibrate, the 1st step is to get the coach level.
When you start an auto level sequence, I think the first thing that usually happens is the front jacks retract a bit. I'd guess they retract to avoid starting the leveling sequence from a nose high position. Then it starts leveling. If after it finishes leveling, the coach is level, but higher than you'd like, let me suggest trying this:
After unhitching and pulling the truck out of the way, manually retract the front jacks until the coach is a little lower in front than rear. Then hit AUTO.
Let us know if that helps.
Re-calibrating will not solve what the OP is looking to do. The only solution is to manually level.
Auto level starts out lowering the nose to get a base line to begin leveling.
If after auto leveling the trailer is too high, manually retracting the front jacks to lower the front may give you two results, one is an error because the rear jacks are already grounded. And 2nd, if it actually does attempt to auto level, since the rear jacks are already down, the end result will be an even higher final level height.
The "brain" does a pretty good job, but it does have limitations. How many times have you had a "green light" yet still have other then 0.0 degrees for level?
How many people even know how to get that reading?
How many times have you had the green light then played with the system a bit, moving the jacks and still having a green light?
The system works great, but the only way to get minimum elevation when leveling is do it manually. Doesn't take any longer (probably even less time) and is just as accurate, just not automated.
Even using auto level to level the trailer then manually lowering the trailer will not yield the best results that you would achieve using manual from the start.