Finally solved the issue :yahoo:
The glass is appearing as intended.
As I said before was tying various things to get the glass to appear. As a last resort I tried messing with the NAMED SHADERS at top the shape file.
shader_names ( 2 named_shader ( BlendATexDiff ) named_shader ( TexDiff ) )
This is how that part initially looked. The first shader obviously for alpha material and next one standard shader for rest of textures. I modified the entry to like this :
shader_names ( 2 named_shader ( BlendATexDiff ) named_shader ( BlendATexDiff ) )
Saved the file, loaded game and crossed fingers hoping that glass appears properly and it did ... :drinks:
Now, I have not much programming insight on how this modification worked but for the moment this seems to work and solved the issue.