Just going to hazard a guess here....

When you have the car raised far enough up that the tires are off the ground then something has to be limiting the movement of the suspension. I'm guessing that the bushings/ball joints/CV joints are taking the streess of the springs pushing down on them. You are also extending the shocks to the limits of their travel. Many of these items are meant to have an operating range that they stay in. Leaving them extended past this range for an extended amount of time will definitely cause problems.

I posted in another thread that if you are going to store your car on jackstands to the frame......it's very worthwhile to get 4 more jackstands and support the suspension a couple of inches from full bottom.