Just to help other people who might be running into a related issue, I was getting some similar issues even after the fix in this thread; it seemed like setting my shader to use Alpha Clip was stopping the depth buffer from writing correctly on objects using that shader... at least, for the purposes of depth blending (for occlusion it worked just fine). I tracked it down to the render type needing to be manually set to Opaque, instead of the automatic "Transparent Cutout". You can find the setting in Shader Forge under Blending, once you disable auto sort.

My understanding of what causes this is that since the forward rendering camera is using shader replacement to render the depth buffer, it's only applying it to shaders with a certain subset of tags, of which "transparent cutout" apparently doesn't apply.