I've seen this gratuitous flickering in a number of test videos. It's very visible in the sky here. The combination (EOS-M / RAW M.L.) seems to have some quirks. Is this a magic lantern issue, a sensor issue, or something else? Also, is there a fix?
It's moderately easy to install. Got to the magic lantern forum. Go on the "camera specific" forum and click on the EOS-M thread at the top. Skim through the thread and you will find multiple places where instructions have been given.