Javascript is just a language, you can write programs or scripts with it to do different things. So someone's written something in javascript that's trying to do *something*. For example, it could be a program searching to see if there's any updates available, etc.
We don't know which startup item is launching this javascript processes, so we disable all to start with. If the window doesn't pop up when you restart, we know one of the items you disabled is the one launching this javascript window.
So we enable the items again, either one by one or in chunks (whatever you'd prefer) until you find that enabling a certain one will start the javascript window opening again. Post back with the name of that startup item wehn you do that.