Any chance there was previous rocker damage? Or perhaps the rockers are not the same. I had rocker damage before and the shop could not repair it correctly for skirt fitment and they needed to cut the rocker off and replace it. I recommend checking the rocker panel part number and if they are the same and no previous damage is present, you may need to add a good quality double sided body tape with a good prepping where the tape will be. If the parts differ, then only replacing the rockers may work for you. Lots of labor involved. Perhaps some adjusting to the back side of the skirts will allow good fitment. Definitely should look for best fitment before final application though, as tape will often let go when done incorrectly.
I wanted to post a pic of mine when it wasn't right, but photobucket is being funny right now.