My 05my Cooper is having a gearbox replaced under warranty. Fault was a misaligned plate somwhere around the cluth, that made a rattling noise when the box was in neutral, clutch out. if the cluth was put in, the noise dissappeared.
It took a BMW Service Engineer to examine the car at my dealer to confirm a new box was needed - it may be that they know there is a fault somewhere along the line, and are trying to work a fix by back engineering the faulty boxes.
IMO, play safe, inform your dealer now, as mine got progressively worse over the course of 5000 miles.
I'd rather be a lightning rod than a seismograph
Ken Kesey 1935-2001