Sounds a little like my experience with my 35i manual. I hadn't really noticed the change properly but sometimes thought the throttle was a little odd as the car would dip in acceleration when gunning it. When i came back from my jaunt around Europe end June/July, about a week later, the engine management light came on, BMW said this was a minor issue to do with mixture and airflow meter but while i was waiting to get the car booked in the engine began to cut out completely. BMW had the car for a week, it took 2 days for the car to take the software upload! I did ask if Microsoft did the coding and was promised they didn't
At the end of the week and £1700 pounds of warranty work later i got my baby back with a 'we're not really sure what it was but we've replaced fuel lines to injectors, plugs, air flow meter etc so she should be fine'. The dealership did say that one of the turbos wasn't functioning properly and the other was compensating for it but they didn't know why.
What you have described sounds very similar to how my car reacted before conking out altogether. I guess mine had been playing up for 6 or 8 weeks before i realised there was a real problem. Silly i know but i just put it down to me not being so smooth on the gas and poss not being used to a turboed engine.
E89 35i manual, deep sea blue, pure white design package, adaptive M Sport suspension, multi spoke 293
'There's nothing so beautiful as the lingering scent of a warm summers day caressing you gently on the passing night air'
, ready to overtake an elderly gentleman doing 20mph 
on a national speed limit road, check mirror, all clear 
, indicate 
.. delayed response in acceleration and a lacklustre pause before the power came through, which never seemed as near the power I have become accustomed to.
