Leaves get transparent while doing one of these things:
holding a single item while in the inventory menu,
displaying the Tab list,
and probably more.
How to reproduce these:
1. Grow/find a tree.
2. Set the graphics [from 'fancy'] to 'fast'.
3. Note that the leaves are opaque.
4. Do one of the above things.
While doing the step 4. you can see that the leaves get transparent, overriding the graphics setting.
Duplicate of MC-57266