Hi Elliot. OK, after looking at your .xcf file I've located the problem. On your "Forest" and "Forest Copy" layers you have already isolated the clouds into forest shapes. I'm not sure if you did this intentionally or if perhaps you forgot to turn of your initial Forest Outline Selection prior to generating your clouds. Either way, what this means is that when you latter followed the steps in the Refining The Forest Outline section, your Blurred frame (set to Multiply) now reveals the layer below, which includes the white background area bordering the forest outline on your "Forest Copy" layer.
The good news is that this is an easy fix. Delete your current "Forest" and "Forest Copy" layers and redo the steps under the Generating Forest Clouds section to generate them again (beneath your "Forest Frame" layer of Course). Make sure you have any selections turned off when you do this. That should do it.