I'm repeating myself, no this won't happen as you are using OnlineVideos the wrong way. The ticks are only to TEMPORARLY disable a site. It you don't want one, REMOVE it from the list. As you have already figured, when a site is broken, it will automatically get unticked so you don't see it, and on autoupdate it will get back enabled automatically when it's working again.
Why are you not using the SiteManager inside MP?
Well the ones you have locally are markes with the "played" color. In my DefaultWide skin this is yellow and the others are white.