The only way we can block in-video ads on YouTube in Safari is by modifying the flashvars before the player is loading. But a while ago YouTube became a single page website, which broke our approach. However disabling the history API forces YouTube to initialize each video with flashvars again. Unfortunately, that approach is very fragile. So when YouTube updates their website there is a chance that is breaks blocking of YouTube video ads with Adblock Plus. This happened twice within the past week. YouTube's latest update was addressed with issue 471
and is currently fixed in the devbuild. We will have a release including that fix later today.