Make sure your mistwood statue guy is out in the open and not surrounded by buildings. I had my guy way in the back of my screen and he was surrounded by various buildings. As soon as I moved him out into the open, my corrupted trees and flower clusters came back. Once I finished my quest thingie, I moved him back so I didn't have to deal with the trees anymore.
i had the same problem...I finally found some large trees at the bottom right of your estate when you are looking at the screen...you have to find a ra mistwood statue to generate trees...hope that helps