Good luck, E53is... I hope they replace that lemon for you. You shouldn't have to worry about the transmission on this car.
I wanted to give an update. I picked up my car today, didn't get the roof rails installed yet because they are still waiting for approval from BMW.
Anyhow, here's the description of the repair they did. "Engine oil pump mechanical failure check function of engine, interrogate fault memory, no relevant faults stored. Connect oil pressure gauge and check engine oil pressure, idle: 2.2bar/4.5 bar while driving. Found noise coming from engine oil pump internals. R&I uppder and lower oil pans and replace engine oil pump."
So, there you have it. The noise is gone for me too. We'll see if it comes back or not eventually. It looks like they replaced the oil when they replaced the oil pump. =)