Custom resource pack: Transparency issue with cloud rendering

I'm working on updating my resource pack, Defscape, to 1.7.2 however I've run into a problem with my cloud texture.

It appears as though Minecraft has changed the way it renders various levels of transparency in the clouds.png texture file.

In 1.6.4, Minecraft was able to correctly read different degrees of opacity, however in 1.7.2 transparency rendering seems to be pretty much completely removed, resulting in sharp, buggy cloud edges.

I'm not sure if this is a bug or intended, but it has hampered my ability to create various transparency levels in the custom clouds.png texture.

To illustrate this, see the attached image.

Left = 1.6.4 and right = 1.7.2+.

If anyone knows a work-around to fix this, that would be great.