I am using the stable 2.0 release with
"overlay_scroll_bars": "enabled"but the scroll bar will not appear on mouseover, i need to move the scroll wheel to make it appear.
As sometimes, I disable the wrap word, I cannot get the horizontal scroll bar to appear! 
I remember before the stable release, the overlay scroll bar will be appear when mouse over it. Hope this will be fixed soon.
I am an OS X user having this problem, too. Before upgrading to the latest version from the previous release, I was able to use my pointer to move the scrollbars. Since there are no longer any scrollbars, I am now unable to navigate through code libraries and efficiently scroll through my code.
As a stylus user, this change has rendered the program unusable. I can understand the thinking behind this (reducing chrome), but the program must be able to facilitate users who don’t have access to a scroll wheel (we do exist!).
I would appreciate the option to enable scrollbars if needed, just as OS X Lion/Mountain Lion permits (or better, for the program to adhere to my system settings).