What's this all about?
Currently, it seems that it is not possible to animate a CSS gradient background image with a CSS transition. This article says that it is possible (at the time, only with Webkit), but I've not been able to get it to work following the instructions in the article.
This is a workaround I used that worked for my purposes, maybe it will work for you.
Instead of animating the background gradient, I animate the background color. I needed to set the colors of the gradient to be partially transparent so you can see through them to the background color.
Since I was then working with partially transparent colors, I needed to either brighten or darken the colors so that their default state matched what was originally designed. I don't have an exact formula for this, I would just eyeball it until it looked right.