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According to 14.4. Fragment Input Attachment Interface,
A subpass input variable identified with an InputAttachmentIndex decoration of i reads from the input attachment indicated by pInputAttachments[i] member of VkSubpassDescription
However, the fragment shaders set input_attachment_index equal to the index of the attachment of the render pass (pInputAttachments[j].attachment, 0 <= j < inputAttachmentCount). Decreasing the index by 1 in all the fragment shaders fixes the issue.
Unfortunately, it doesn't seem like the validation layer catches this issue although there seems to be code for it at layers/core_validation.cpp:2652 . Do you think this issue has enough information to file an issue with the validation layers?