U joints wore into the pattern of how the joint flexed at the stock height. Lifting it moved the pivot spots and the joints are moving from a worn spot to a non worn spot. Try replacing the u joints and the problem should disappear.
EDIT: Moonshine beat me to it!
90 YJ 5.2 Magnum, AX-15, 231 SYE'd
D44 front, welded/trussed AMC20HD rear. 4.56 gears soonish.
Western 6 lug aluminum wheels, with 35x12.50x15 Wrangler MTRs