I had the same problem with my fronts. It took awhile, but I finally figured out the problem. The directions mention using longer bolts in some of the top center holes in the flare...don't! If you look inside you'll see the longer bolts go through the flares and clips, and then when tightened down they continue through the clip and hit a fender support. As they are tightened further they push against the fender support and push the flare outward. This pushing on the top center is what causes the fender to bow and not sit flush with the flare. This is also what causes problems with getting bolts into some of the other clips. As a temporary fix you can just loosen the longer bolts and try to get your fender to flatten out (mine woulnd't and was permanently bowed). As a more permanent fix you can pick up a few more of the shorter bolts.
The worst part is I described the problem to PSC and asked them to look into it and get back to me. They never got back to me, never changed their directions or their bolts, and people are still damaging their Jeep's front fenders.