SkBee recently added a config option for scoreboard lines to be reversed or not. Currently, this needs to be set to false otherwise the scoreboard will look funny. In the future, this will be handled automatically by the script, no matter what the config option is set to.
Added:
New and improved scoreboard! It now shows more information, and allows you to cycle through the lines by scrolling in your hotbar while sneaking and holding the Cookie Clicker item.
Now awards AFK cookies (when you log back in, you'll be given the amount of cookies you should have received in that time)