In build 1.8.2 there is an issue with transparency maps - they won't render entirely transparent. 
There are two workarounds for this: 

1: Use a Standard Material

2: Use the übershader  - it will render correctly, depending on your mesh. However, if you're rendering foliage, you may run into an issue where only squares are rendered as shadows. If that happens - switch back to Standard Material

This issue has been reported as a bug, and is on the fixlist