I read through the thread Michael mentioned too, and was abel to add the fade between basemaps tool to my SFV 1.3 site. I've made a few changes and it works fine.
But there is still one thing annoying me that I haven't solved yet.
When you change the basemap from the map-menu the slider doesn't move. I looked att the function that was changed in the mapmanager (basemapMenuClicked), I guess that's were I want to change the value of the slider. But the slider is added in index.mxml and I don't know how to access it from the function in mapmanger to change it's value.
Another solution would be to just remove the basemaps from the mapMenu, I don't really need them there anyway since I've got the fader tool to control the basemaps. I tried to accomplish this in the config.xml without success. Tried remove them or even move them to another menu, but they still appear in the mapMenu.