The gradient transform tool will only work on a shape that is prefilled with a default gradient (like the from black to white one).
It will stay "dead" if you try to use it on a shape that has a simple colorfill.
I'm having similar problems with the Gradient tool. I'm on a iMac 2009, OSX 10.8.3.
The gradient transform tool isn't working properly. The options for the tool aren't showing up in the tool bar.
I want to transform a gradient in multiple elements at the same time. A bunch of letters in a word.
The gradient transform handles only show up when I select a single element. And not when I select multiple items with the same gradient fill. I'm also using Flash CS6 via Creative Cloud.