When you have a transition on a background with webkit-gradient it doesn't transform properly. In the example I have attached the transform does nothing when applying a gradient, and when you remove it. It will pop to the to colour of the gradient and then fade to the background color.
Created attachment 62476 [details] Example html code
background-image doesn't support transitions. background-color does, and your example is animating it from blue to transparent. So this is working as designed.
*** Bug 46082 has been marked as a duplicate of this bug. ***
*** Bug 42274 has been marked as a duplicate of this bug. ***