Well, that scale thing might not be true... If the trees first render, and then get covered by ground, they are being rendered.
I have had this problem with my forst (and so far only) tree population.
There is definetly a bug in there somewhere, and the solution is a bit of trial and error...
When the instances show up in the preview window, try moving your camera down. Are they really on top of the landscape?
If they are in the preview, they still might not be in the render. What you have to do to fix this is change the location of the main tree that is being instanced. In the opjects screen you have "Pop tree.tgo" and "Pop tree.tgo/tree.tgo" The last one being the main tree. If you change it's 'y' position, your entire population should move according. If you change it too much your trees will be high up in the air.
Work with trial and error to get the right y position.