RMaguire,
No paint adhesion problems. I ordered them from ATS pre-painted and they matched perfectly. They attach with 3M body tape which keeps the flare from rubbing the paint and screws into stock holes inside the wheel well. I have had a problem with the passenger rear flare, oddly enough, which has separated from the body slightly due to the tape not sticking. I think that particular flare needs to be adjusted in terms of position on the body and it's probably my error installing it. The dealer also treated my truck with some kind of teflon protectant without me asking for it and I did my best to get make sure the surface was clean, but I can't tell if I got it off or not. I forget what I used, but it was a wax remover of some kind. Weird that it worked on 3 out of 4 corners.
Overall, I'm happy with them and they way they look and protect the truck. I also have 3M Paint Protectant film on my rockers. I took the truck on a fishing trip up to Maine last fall. We drove 15 miles out on a logging road to get to camp and I could hear the rocks smashing into the rockers the whole way (I have no mud flaps). I was cringing the whole time. My Dad and brother are telling me "boy don't you wish you had mud flaps on there now", and "Wow, you're going to have some huge chips in your rockers!". I couldn't look while we were up there, and after we got home (another 15 miles on that dirt road later), I washed the truck and low and behold, I couldn't find a chip on there.