Thanks to everyone, who posted. To answer the question someone asked above, about the noise - it is like a slight, faint clatter. You can only hear it, when you release the clutch in neutral (for maybe 1-2 seconds). Again, I did not think that it was anything serious, since it drove fine. I simply mentioned it, and asked if it was normal, when I dropped the car off for some other warranty repairs. Little did I know, it would have turned into this.
I got an update from the Dealership on Friday. My service writer said " this is going to sound crazy, but I received a call back from another master tech at the M factory. They still think it is a transmission issue."
So they are going to order a 3rd, brand new transmission to install. She said the transmission will take another week to get in, and a day to install. She also questioned the mechanic doing the repairs on my M, and asked him if he has ever seen or heard anything like this before. He has been with BMW for 31 yrs., and said he has never replaced a tranny on the same car, more then once.
The saga continues....
I'll keep everyone updated. Thanks again.