Semi-transparent textures become fully transparent when using a resource pack

The issue:
Semi transparent textures, like stained glass, become entirely transparent after a few seconds, except for the opaque parts. When destroying any block, it becomes normal again, to return back to entirely transparent after a few seconds

Demo:
http://youtu.be/PYr_wqYt7oU

How to reproduce:
Load a world with the attached resource pack. It has custom stained glass. I have been able to successfully reproduce it in a redstone-ready superflat. See attached screenshots.

Additional:
I tested whether it is chunk related, but that does not seem the issue. You can break any block anywhere to restore the normal texture, and vice versa. It seems related to the texture atlas.