Did you try a clean reinstall of the game?
Which tree are you at? For the tree on the island near the start of the fjords, try climbing up the ladder and entering the treehouse. Leaving there may trigger the appearance of a goblin (though you can not interact with him until after talking to the tree), which could conceivably make a difference dealing with the tree.
Have you tried talking to the second tree, north of the north east end of the long island in the middle of the channel that leads to the harbour? (ie across from the entrance to Stone's flying fortress)
