I too have suffered the issue with creaking seals. I suspect it started after a complimentary reconditioning at the dealer, but I am still at a loss regarding what exactly is causing the issue (cleaning agent, drying, etc.).
Anyway, my problem seems to have been fixed after the dealer replaced all the seals (both inside the doors and the seals on the upper part of the doors). This was after two previous attempts of cleaning them.
So I would definitely advise you to not give up on the issue and insist on the dealer replacing the seals.
If anyone knows what might be causing the issue in the first place I would be very interested in learning about it. I would definitely like to avoid this happening again.
Melbourne Red F31 328 M sport