I have a large problem with my worldspace whereby the tree LODs aren't displaying correctly (see the picture below).

http://imageshack.us/f/845/2013060300001.jpg/

You'll see in the picture that some LOD trees have a dark rectangle around them, and some of the LOD trees have half of the tree missing.

It's a large worldspace and so I'm running the tree LOD script fix in TES5Edit on the BTT files after I generate the tree LOD in the CK to counter the wall of trees problem at the 32 cell border.

I'm using the latest version of GKB trees also. I was previously able to generate tree LOD just fine, but for some reason with installing the latest versions of the GKB trees, I have had these problems with the tree LOD. As no one else seems to have had similar problems, it must be something I'm personally not doing correctly somewhere along the line (maybe with the installation of the GKB trees, I don't know) but I've been trying to figure this out for a while now.

Any help on where I could possibly be going wrong would be appreciated.

You must use tree atlas provided with GKB trees renamed to your worldspace.