I tried that tutorial a while back and, as far as I can recall, it still works pretty well with Gimp 2.8. I doubt the software version is the problem.

Daxian, I suspect you've drawn on the wrong layer at some point. It's very easily done. Have you tried clicking the little Eye icon next to the layer name for each separate layer to make sure that what's supposed to be there is actually on that layer? If your trees disappear when you turn off the background, you might have drawn them on that later by mistake. Another possibility is that you've got some sort of layer blend like Multiply or Overlay set for your tree layer, and it needs something other than a transparent background to show up. If you make sure your layers are set for 'Normal' blend, does that help?

I can't remember every step of the tutorial unfortunately to be more precise with what might be wrong, but I hope you figure it out.