The shader "mod" was simply an adjustment of the existing shader file that handles lighting.What was actually changed with the new shader? I know glass now looks a lot more glass-like (less see-through and more colour) and that everything is less reflective. Has it got anything to do with the shader mod you released a while back?
The latest version of the game now has those adjustments (more or less).
No additional code was added to the shader, it was just a case of finding a more suitable balance of the variables.