I was experimenting with LPV and the new DF shadows and my sample SpeedTree lost its leaves too. I didnt pay much attention to it, I thought it was because the engine was generating distance fields. I had setup too high a resolution, and I had not enough patience to wait for it to finish, so I stopped it and deleted the project.
Maybe thats a hint why your leaves are gone.
Else its a hint that something in 4.5 is broken.