Do the ladder bars have an adjustable link on the lower rear portion of the bar? If so with the shocks off, if one side is hanging lower the preload may have been set differently than the other or something is binding up. It is typycal for the driver side to be lower than the passenger side, not the other way around. There are many scenarios which could cause this. But I would start by ensuring all the rod ends are adjusted out equal amounts. If it still is an issue, start looking at bracket mounts on the rear end housing, maybe they aren't in the same location on the housing.
Bill