I took a quick look at it. It reproduced with the renderdoc capture but I couldn't see anything wrong with the problematic draw.

Looking at the first draw where these black squares show up:

• shader outputs are roughly the same between an affected pixel and a neighboring unaffected one
• depth test & stencil test are both fine
• No discard/demote in the fragment shader
• Shading rate of the pipeline: 1x1, combine ops: Keep, Max
• It doesn't write the shading rate in either the vertex or fragment shader
• no TCS, TES or GS shader
• the affected (black) pixels match up with non-zero pixels in the shading rate attachment (values are 1, 4, 5)
• unaffected (correct) pixels match up with black (zero) pixels in the shading rate attachment