Transparency acts strangely with resource packs

When using a resource pack in 13w41a, some semi-transparent textures (i.e. ice, stained glass (shown)) will not display correctly and will be completely transparent.

How to reproduce:
1.Place some stained glass or ice in your world. Note that it is tinted with the default textures.
2.Use a resource pack that has a semi-transparent texture for stained glass.
3.The semi-transparent parts will flicker between semi-transparent and completely transparent. This seems to be connected to particles somehow (For example, the blocks retain their semi-transparency as long as there are particles on-screen)