Okay, I tried a couple of things. Since the leaves were upside down from the model you gave me, I opened the tga in Gimp and did a save as and set the origin for the lower left again. After I rebuilt my tree and imported it, the leaves were then the proper side up.
However, even with no actions attached, I still get that sorting problem. With the actions attached, the same thing, though the lighting on the leaves changes if I attach a material or not (with the material, no extra lighting, just ambient).
I have the shorter wiki script currently in my tree1.wdl. Tomorrow after work I'll try the longer script from the wiki and see if that makes a difference.
Just out of curiosity, what did you do to the tga to make it different? I noticed the size is larger, but I couldn't tell what else was done to it (other than the initial upside-down leaves). I'm new to using tga's...