If your lift involves either a body lift, or t-case spacers, your shift arm is pressing against the boot, and thus not getting full range of motion. I had the same issue after i lifted my TJ, but its an easy fix.
If you look at the shift lever, it is angled down at the bottom. Since the position of the transmission, relative to the boot/console was changed if you lowered your tcase, the angled portion of the lever is hitting the boot when you go back into reverse. To correct it, just take off the lever, place it in a press or vice, and slightly straighten the angle of the bend. Dont go too far, only about a half inch will do the trick. If you co too far you will be hitting your hand on the bottom of the console when you shift into 1st, 3rd or 5th.
This theory is easy to test, too. Just remove your boot and see if it helps.