I saw this thread a while ago and keep forgetting to reply. I had the same battery discharge message pop up on my 35i and had to take care of this outside the warranty. I took it to my local dealership and got a quote; can't remember the exact number but I do remember it being significantly more expensive than a local Dinan shop. So I took it to Dinan and paid $421.22.
This price included switching to an AGM battery, which was done at my request. Dinan would have been content to switch to a conventional battery at $270, but the dealership had recommended the AGM battery because of the discharge issue. It might be a comfort access thing, or it might be related to the V8's same problem, which apparently is a combination of the engine being engineered to charge the battery only when coasting and a fan having to run when the car turns off in order to cool down the big V8. Unbelievably, the V8 apparently has to change its battery with every oil change! See:
http://www.roadandtrack.com/car-cult...ns-bmw-n63-v8/
The battery was switched out in November 2014 and although I haven't had a discharge message since, I have experienced occasional odd electrical gremlins, like the mirrors resetting themselves. Hasn't happened in a while, so I'm wondering if that's a product of cold weather.
Anyway, hope that info helps you or anyone else dealing with this problem.