I have had a similar problem with irregular wear on the surface of the rear discs. Front discs are always clean on the surface. I have always suspected there is an issue with the rear brake setup.

 

Nah. In general (not the OP's problem) Rear brakes see very little duty so they won't wear as evenly as front brakes, particularly if you drive gently and/or seldom. So you'll get "streaks" on your rear rotor showing uneven areas of contact. Nothing to worry about. brakes are fairly simple and there's not much that can go "wrong" with them. Just brake harder so you get the pads to wipe away any streaks. Many times, perception is the real problem.