I was just reading a post ( http://board.phpbuilder.com/showthread.php?10385281-Directory-file-structure-critique ) and found myself enable to scroll down in the code div. I had to pimp the div height in DOM debugger.
I am running Chrome Version 20.0.1132.57.
Which O/S? Scrolling worked fine for me in the same version of Chrome.
MacOSX Snow Leopard (bit behind on updates, despite the nice USB drive with the damn update on my desk for the past year or so).
Actually, never mind. I just checked and now it works...
It's the gremlins at work again. 
Speaking of the scrolling, one enhancement suggestion I would make is to give the PHP/CODE/HTML/etc. boxes an "overflow: auto" so that the scrollbars would only be present if necessary.