I also have this problem. I have been talking to Apple Support for over a week. It only happens intermittently and only affects the keyboard. It was OK with a wired keyboard but yesterday that was the same too. I found that unplugging it and plugging it back in again resolved it, and also that switching the keyboard off and back on stops it (till next time!). With Apple support I have deleted loads of cache files, reset the SMC and reinstalled El Capitan, and it is OK for a day or so and then starts up again.
Given that a number of people have not reported this issue on the Communities, I suspect it is an El Capitan issue and just hope Apple get to the bottom of it soon. I now have a Senior Support Engineer working on it.....