I am currently designing a resource pack, and one thing it does is make GUI's transparent.

Note: In the screenshots, I was using mods on 1.7.2. However, this issue happens in vanilla 1.7.2 and 1.8 as well.

I started with the HUD, the menu buttons and creative inventory GUI, which I was able to make transparent just fine (Screenshots 1 and 2, the squares on the backgound of screenshot 2 indicate transparency in image editors).

When I was done with that, I went onto designing the rest of the GUI's, which were the block inventory ones (anvils, beacons, chests, etc...), however, the GUI's on these are not keeping transparency (Screenshots 3 and 4).