bigwave, I have the EXACT same problem now for two year sand I CAN NOT solve the issue. I've tried everything other than removing the sheets of glass and re-doing the rubber surround, which I DO actually have and may do this winter.
I have removed the rubber accordion boots on each side of the large glass sheet to inspect the screws for looseness, and NOTHING, but it seems like thats the issue. press up on the glass when in closed positiona dn sound goes away, seems like it just needs a fine tuning somewhere. I've tried rubber tape, re-initializing time and time again... I have removed the entire headliner to look for loose screws in the cassette and nothing. and let me tell you, taking the headliner off is easy kinda, but a time consuming process for sure.
I've researched for about a year, and even posted in many thread about solutions to this all too common issue, but no one seems to have a solution other than just buy the kits and replace.
I'm wondering if I just need to buy two new kits like mcurcio has to do as well and just bite the bullet. Once I get it fixed, I'm not using it again haha. HATE My e53 cause of that rattle. I've often debated selling it because of this rattle. And it gets extremely worse in colder temps, so I'm crying now as I drive it in winter.

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I swear, my cars are like a girlfriend.
Sometimes its a rough ride, sometimes its smooth motorin'.
Sometimes she doesnt like how i treat her and sometimes i dont like how she behaves.
BUT at the end of the day, she loves it when I am inside her.

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'91 850i
'05 X5 4.4i
'09 Clubman S