I agree. It seemed odd that the problem started immediately after changing the plugs, even when using the exact same BMW plugs, but maybe they had it dialed in just right. I am about 2k past my change of plugs and recently just took the car in to get the software update (I am 2 years removed from warranty) and paid to see if that would help as the SA suggested it would, along with my Indy Mechanic, who worked for BMW for 35 years. It actually made the problem worse. Now I feel it on the freeway slightly and it is much worse when starting the car warm. It will hunt between 500-900 RPM and almost feels like it is going to stall. This car ran smooth for years, so I'm not inclined to agree that it is just the car. However, you, myself, and many others have tried numerous solutions without any luck. I prefer to change plugs around that same mileage also. Not a big cost, and doesn't hurt anything, I guess except for when it gives your car a random rough idle with no code...
I forget, did you ever try that reset of adaptation that was recommended by causing the car to throw a misfire code?