How it works is that once you start getting these Server Side Ads (SSA), Youtube will create a sort of queue of videos in place of your usual video, with the first few being ads that can't be skipped and have a red bar (not yellow) and in the end you'll get your video. They are not literally part of the original video stream, they are separate streams that get injected as if they were the original video. It's called SSAP, and I've been experiencing it from the last weekend. In the meantime, they've pretty much broken their player to implement this.