Here is another test you can try. You should have the truck available so that after doing this you can set the trailer back on the truck and raise all the jacks so you get back to a 'neutral' frame level.
Level the trailer front to rear with the front jacks.
Try lowering all four rear jacks at once with the "rear" button. Bring all the jacks down till they start to lift the trailer.
If that doesn't work because the jacks hang, make note of it.
If the all "rear" jacks doesn't work, lower the left and right sides until they just start to lift the trailer.
Once you have all the jacks preloaded, try and manually level side to side. If you push either the left or right buttons you will see the screen change to the degrees out of level.
Assuming you can do this means the jacks and pump are in fair shape.
Next test would be to start raising the trailer all the way, till the jacks run out of stroke.
Sometimes you can do this with just the rear button sometimes you will need to alternate side to side.
Using the rear button only will only move the middle and rear jacks
Using the left or right button will move all three jacks on that side.
Do this until it is obvious you have no more lift.
You should be able to get the the trailer several inches off the ground doing this.
If you can do this, that should mean your 12 volt power is sufficient and the electric pump and hydraulic side have the necessary capability.
Bent or sticking pistons will cause the problem you are experiencing. In any of the auto modes, the pump will run until a set amount of resistance is achieved, then switch to the next sequence.
If your piston is sticking, the circuitry may be reading that as a "grounded jack".
Note, that after doing the above test, your trailer may have a slight twist in the frame due to all the jacks being extended to max. Hence the reason to have your truck available. Put it back on the truck and raise all the jacks to unload the frame.
Another note, the best way to come off of an all jack, max extension, trailer off the ground scenario is to use the "all retract" function. This will activate all 6 jack release solenoids at once, which results in the least shock to the system and trailer.
As you do this - once the rear tires are on the ground and all jacks are still retracting hit any button on the controller which will activate an emergency 'panic' stop of the system. Some systems you can just hit enter to acknowledge, some you may have to turn the controller off then back on.
Give it a whirl and report back.
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Another consideration, the Lippert controller tends to be a little voltage shy, meaning if it sees low voltage it kicks out. What I found with mine is that the Lippert controllers battery voltage reading is .5 to .6 lower then actual battery voltage, giving it a false low voltage error.
The controller doesn't know how far a jack is extended, what is does read is how much resistance the pump is generating as it runs a jack down. A piston that is sticking will cause a higher pump resistance.
I have discussed this with Bob Teague and he is aware of it, but never got back to me with a solution.