Just had my new Magnaflow exhaust installed at the Mini dealership (I do not have access to a hoist, and I am just too freaked out by confined spaces to crawl under the MINI!), and it sounds awesome.
Well, let me qualify that. The PIPE sounds awesome. Unfortunately, due to a design flaw from the folks at Magnaflow, the constant buzzing produced by the hanger rod near the front of the pipe (nearest the cat) rubbing up against the tunnel wall of the MC is freaking annoying!
I took the MC back to the dealership, and they pointed out the problem and applied a fix which I hope keeps working (not sure what they did, but the buzzing stopped - think they jammed a big rubber bumper in there?...)
You see, it appears the people who designed this little noise maker did not look closely enough at the stock pipe and take a que from its design. The stock hanger rods (both) are equipped with - for lack of better terminology - a wider "flange" (?) which seats the hanger rods in the hangers and prevents them from moving too much to the left or right. For some inexpicable reason (?) Magnaflow designed this pipe with these "flanges" at the back hanger rod (nearest the exhaust exit), but not at the front hanger rod (nearest the cat). Consequently, the pipe can move left to right enough for one of these hanger rod ends to rub up against the tunnel wall and vibrate like hell!
I called Magnaflow's Tech people today, and although they seemed empathetic to my problem, offered no solution, and simply asked me to call back if the problem persisted. Hopefully, nobody else experiences this problem, although I am fairly confident in time you will. Magnaflow has been made aware of the issue...now lets see if they actually DO something about recifying it (?).

 

I dealt with it by having it lifted and by pushing the heat shielding back away from the exhaust piping, etc. Try to get access to a lift, or get a really good jack and go under the car. If you rev your car next to a wall or curb you may be able to make a better guess at where the vibration / rattle is coming from as the sound will bounce back to you in the car.

 

Same approach as Scott. It took 2 tries to get the heat shield far enough back, but it has worked like a charm for the last 18 months.