Something strange I've just recently noticed. New labels generated don't contain the icons. It just has the 'dot signal' icon. Is there a limit on how many? or how far? or number of surfaces? I'm playing with SE so I don't know if that has something to do with it, but at least not initially.
If I start a new game it works fine. Icons are generated with the patch size (like your screenshots shows). But it stopped doing that sometime.
I've tried it against a dev's game to confirm and his show the same 'issues'.
This is reproducible for me. Only difference is, I'm running the latest factorio version (and all the mods) from his original post.
1. Loaded and sync all mods and settings as the dev's final save game. ( https://imgur.com/a/LdR58ep )
2. View Nauvis ( Just in case you aren't familar with SE... from his save, hit U, Nauvis, View Surface )
3. If you scroll around in map mode, you can see the patches with icons near your initial spawn. But farther away at the edges of the revealed map they are just 'dot signal' icons. So unless he changed them himself, I'm assuming it's the same as what I'm seeing. This is especially noticeable on the far east side.
4. Just for checking, I tried on a newly generated surface/planet. ( Same U. I picked the last listed with resource, 'Galactic Gravel' and viewed surface) Same dot icons.
I do have my save but it's more modded and I wanted to be sure it wasn't something else. The Dev's save game is minimally modded at nearly just vanilla SE. Again, I don't know if this is a SE/surface issue or not. As I have started a brand new SE game and the icons generated fine. So while playing, sometime during gameplay it stops.