Hi I haven't played the game for a while and I might be wrong here or even got the wrong end of this thread, but I think your having this problem because of the world grid, the buildings that you have got originally placed are not placed on the WORLD GRID at the beginning.
So when you come to place the protected area which confines with the world grid you end up with your problem.
Again I might be wrong here but going by your last screen shot that is what it looks like to me.