Chrysler released a internal bulletin on owner modifications and warranty with a list of items to look for. Lowering springs were listed and stated that they change the suspension geometry and this can cause premature wear to the tripods and damage the CV joints and reason to deny warranty.
They did mention that the MoPar springs use a stop ring limiting the the amount of lowering. It does not specify whether the warranty claim would be honored with use of MoPar springs but it most certainly could be interpreted as such.
I would find out how much the MoPar springs lower the car and compare that to how much your springs lower the car, if they are close then you have a legitimate argument. Print out the section and take it to the dealer. Good Luck!
http://www.agpturbo.com/images/aftermarket.pdf