I had this problem after installing the Calmini 3" lift. I haven't completely fixed it yet, but it's better. Yes, it seems to be caused by the angles of the U-joints at either end of the rear driveshaft not being equal. It's very hard to "eyeball" the angles. After messing around with trial and error adjustments, I decided to get serious.
I purchased an angle finder (a whopping $8 at Harbor Freight Tools) and pulled the driveshaft (easy). I used the angle finder to measure the angle of the output flange at the back of the transfer case- in my case, it points down about 6.5 degrees. I adjusted the heim joint until the flange on the differential pointed up by 6.5 degrees- at this position, the threaded rod on the heim joint was backed out about 10 threads. I still need to do a bit of trial and error to optimize the position, but at least I know I'm close, and things are a lot better than they were before. Calmini's recommendation is to start with the rod screwed in all the way, which on my vehicle was way off.