Think of the auto level as more of an auto stabilizing system. You need to get the trailer pretty level before using the system. If there are any low spots build them up with pads or wood under the jacks and if necessary under the tires.
Think of the "out of stroke" message from the system as one of the jacks (or more) can't extend far enough to do its job of getting that portion of the trailer level. Just like if you had traditional hand crank jacks and one of them extends down all the way yet doesn't touch the ground.
When the system goes into the out of stroke mode, it stops all jacks, so if your middle jacks are not coming down, it tells me that on one of the four corners the jack has extended as far as it can go and halted the system.
Using a traditional level on the floor or counter you can tell which way the trailer needs to do, retract all the legs (except the front two) build up under the jack that has extended to its full stroke, then try again.
We mainly dry camp or boondock, so I never have a very level surface, I carry blocks to put under jacks. Once you get the hang of how the system works, you will LOVE it.
I hope this helps?
2012 Epic Voltage 3905
2013 High Output Dodge Cummins