When I try to use the BlusteryDay shader resource pack provided to test out the shaders functionality newly introduced with my custom resource pack the shader doesn't work. Might not be much but it could indicate a problem.
I changed the float animation constant multiplicator to make the aniamtions slower.
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It appears the BlusteryDay shader checks the block atlas to check if the block texture uv is correct, to ensure it only affets leaves, etc and not also other rendertype_cutout blocks. This means that if you have a non 16x16 texture, it will offset the uv from the expected loc for 16x16, and skip the if statements. However, as of now, there is no better way to check the block than just using the texture id, which (as seen here) is rather fragile
Are you using the Fabulous setting?