I fitted a full Milltek system to my 1M and think I may know what the problem may be....
Do your right hand side tailpipes sit higher than the left side? And my guess is that the pipework is very close to the small metal bracket on the left of the rear diff housing?
If so the system sinply hasn't been fitted properly. All of the sleeves need to be fully pushed home and the mounting in the near to the centre section is adjustable. Once the system is installed and aligned properly there is no noise, clearence to the diff is perfect and it sits level on the rear. I know this as I had the same problem on my car after a rushed installation so I took my time the second time and its now perfect.
AW 2011 1M, Gloss black GTS alloys, Milltek full non-res system, K&N Sports Air Filter, Eibach ProKit springs, Michelin PSS Tyres (Front 255, Rear 275), BMW Performance grills, BMW Performance pedals, IND Gloss black side repeaters, Carbon Fibre Rear Spoiler, ABP OBD isolation, LUX Angel Eye upgrade, Venture Shield kit, Lightweight front splitter, BENTLEY Alcantara steering wheel (Orange marker & stitching)...