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.