although my car isnt lowered, my milltek exhaust did rattle when i first fitted it, and it got worse when it got hot as it causes the metal to expand. i think in the milltek instructions it says the entire exhaust system will be 15mm-20mm longer than whe cold... somethig like that anyway... anyway, i took my car back to milltek and they sorted it for me, took the backbox off and cut off the pipe where it goes over the beam and welded it back on slightly rotated. this has given PLENTY of clearance on a standard ride height, and it may be enough to stop it knocking on a lowered one, or maybe atleast make it better!?!? just a thought.
their workshop was in ilkestone, near nottingham by the way