Ok, found the fix. In the Render Settings > Options > Level of Detail, set it to 100% (Anything below 95% results in the issue you were experiencing).
I don’t know what’s going on there, but since Level of Detail (see the help) refers to subdivisions, perhaps it has something to do with the “Subdivision Manipulator” that appears in your Filter view. I have never seen that before, and can’t find it in the help. I’m guessing that some setting is affecting the subdivisions of the clones, and your original setting of 80% in the Level of Detail caused the issue of missing clones. I’m at a loss to explain what’s going on there, but perhaps someone more knowledgeable will chime in.

