Dithering shaders don't work properly; colors are messed up

This is my first encounter with Retroarch. I’m playing Genesis games with the Genesis Plus GX core. They look and play fine, but when I enable a dithering shader colors get completely messed up. This is what it looks like with GDAPT:

This is how it looks with no shader:

What am I doing wrong?

Hmm, seems to be working fine here. Which OS/platform are you on? Which video driver / shader type?

Windows 7 64-bit / Retroarch 64-bit. gl driver / both cg and glsl shaders.

The last time somebody said shaders were doing unreproducible things, they had video filters enabled, that’s the first thing I’d look at.

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I haven’t even touched filters yet.