Don't know what's going on with the tree and this is probably long sorted but a few people have had this issue with the background. If you make a lot of modifications with your terrain, particularly fractals, then your entire terrain will either rise up or lower down but your atmosphere will be unaffected by it which means that it is still set for the default terrain settings. This is so because the atmosphere will then scale correctly for high altitude scenes, but if you raise the terrain, pretty much, unwittingly then you'll need to adjust the atmosphere to accomodate it. As Edlo said, haze density, bluesky, additive all need to be adjusted proportionately to how much your terrain has scaled.