If you create an addon on Builder, and click the little 'v' button next to the save button, you get a little flyout menu that lets you select a version number and a commit message. After you set the version number to something you choose, if you click the Save icon, the addon will be saved with that version number. But if you hit the 'enter' key, it seems to just reload the page, reverting your change to the version number back to "initial". It should probably just do the same thing as clicking Save. Not sure if it's a bug that it isn't doing it, or if it's just something that never worked. I don't remember offhand if this ever worked in the past.
The builder project has been discontinued as of April 1st, 2014. The announcement last year: https://blog.mozilla.org/addons/2013/12/18/add-on-builder/ Next steps (still being written): https://developer.mozilla.org/en-US/Add-ons/SDK/Builder