Brian Boellner

This issue has been noted under Mojang's known issues list stating "Flipbook textures do not support MER and Normal textures"

This is mainly due to the default texture being stored as a PNG file.  I'm assuming the back-end is "guessing" for transparency when working with a transparent PNG.  However, when switching to a Targa (TGA) file format for the texture, you can get the glass to look much better.  Short term the dev team might change these textures over to tga files instead of png files.