I paint the trees on to my terrain and i can only see the top of the trees coming out of the terrain, and when i look underneath by terrain the rest of the tree is there. And no I am not upside down.
I did a little testing with Unity’s standard “Big Tree” and found absolutely no problems with its position on the ground. I raised and lowered the levels of the terrain and they were still fine.
The problem may lie in what tree you’re using. I know that if 3D models aren’t correctly positioned (or centered) before they’re imported, they can appear in any place other than where you want to put them. If you’re not using “Big Tree” already, give it a shot by going to Assets>Import Package>Tree Creator.
If the problem still persists, I would restart Unity. That’s all I have, and I’m sorry if this doesn’t help all of you out.