Okay these are just random thoughts im gonna throw out there... forgive me if some of it seems silly or basic.
The point about the locker i was getting at is if you're measuring the suspension say after you turn into the driveway, on the throttle, the locker can preload the rear springs and make it lean while its parked. Welded/spooled rear does this really bad. Not an issue if you're open.
Did you torque the spring/shackle bolts down after you got it down sitting on its tires or did you do this while on jackstands? If so, the springs/shackles could be bound up slightly causing the lean.
Are you driving it around first and then measuring, or measuring as soon as you get it down off the jack? You should drive it a bit and see if it settles out before trying to fix it.
Run a tight string from the center of the front leaf spring bolt to the center of the rear leaf spring bolt at the shackle. Measure from this line down to the Ubolt plate (find a common point that is inline). This will tell you for sure if its a spring... if one has more arc than the other then either they arent a matched set or you have some kind of weight balance issue. Drive it around first before you take this measurement.
If all else fails, swap the driver and passenger leaves with each other, drive it around and remeasure.