All hexheads have this flat spot to some degree or another. In my experience, the R12S has a more pronounced flat spot than most. This is a bike that is tuned for power from 5k-redline.
Like others, I chased this problem but never completely eliminated it. Read my experiences tuning with open pipes, FRK (air temp spoofer) and Power Commander 3.
http://forums.pelicanparts.com/bmw-r1100s-r1200s-tech-forum/613717-r1200s-dyno-tune-results-full-remus-pc3-frk.html
The AFR shows a rich spot in the stock map through the flat spot. Some of our German friends believe this is a problem originating in the air box and not fully treatable without addressing that part of the bike.
Regardless, while I'm sure Ralf and Co. found some improvement with fueling, every dyno map I have seen on this engine (regardless of fueling or pipes) has this flat spot. Even the mid-range tuned R and RT bikes. It's just exaggerated on our R12S hot rods.
IMHO, YMMW, FWIW, and all that.