Commonly known as "exhaust soot" which is the norm. I've always been taught that it's due to Incomplete Combustion
I''ll tell you this about exhaust soot build up on your pipes: One, is clean them whenever you see them visible. A wipe-down with a MF or Terry towel with some GC or AP cleaner is often suffice. Leaving them for any prolonged period before wiping them clean will create a film on your tips over time that need to be polished out.
Two, is after cleaning them [preferably following a wash] apply some clear-coat sealant, wax or an equivalent product on the tips. This will give them a protective film that will make them a LOT easier to clean in between washes.
Not sure what you're saying re: the paint damage.... Did the new pipes cause the paint damage? If so then they're either too close to the bumper's lip and the pipe's heat dissipation is causing the flaking and/or they're not mounted rigidly enough [incorrectly] and the vibration is creating the flaking. Read: They're getting too close to your bumper's lip.
Exhaust tips will generate some serious heat under extreme conditions. This is one major reason why I'm a fan of double-walled tips over the paper-thin single layered.