Minecraft 1.6.4 - Forge Mod. Created 5 new cookies for in game, including art and a new furnace/suntable; two new trees, a peanut plant, and grape vines.
This is still an issue. It just prevents the transparency. But leaves don't function how vanilla leaves work, having transparency for sides but not through the whole tree.
Leafs of both trees are completely transparent. (Can see through the ground)