You need to connect a harness directly to the battery to charge it and bypass the BMW CANBUS system that is completely different than the electrics we had on the 1150R.
(I miss my KISSAN signal minder! I want the turn signal to be running lights again!
That should help as I don't believe you can charge the battery through the R1200 BMW powerlet socket, unless it's hard wired to the battery. (doesn't come from BMW like that)
Something like this:http://www.ascycles.com/detail.aspx?ID=48079
Once you have an SAE harness installed, that's what you could use to plug in an air pump or electric gear, as the new and improved CANBUS powerlet socket won't support things like that.
Or buy a Shorai battery and never need to worry about plugging it into a charger. I have one on my GS, super lightweight, strong cranking power and will hold a charge for a year without a tender. Mine was just left untended for 4 months and started like it was ran yesterday. I've left my 8" HID race light on for 2 hours (not wired into ignition) and my bike still started, it's that good. http://www.shoraipower.com/