I have found the same to be true for the Nuclear Plant world object. The fault is probably in a graphical shader (or two) not using the sphere-warped coordinates.
Here are three screenshots of me moving closer towards the Nuclear Plant building:

The Building skill affects only Stone Well (which I've never seen) and Campfire, according to the skill's description. Logging skill should only affect the process of chopping down trees - although a friend of mine who was leveling this skill did not see any gains. Rough Cut Lumber appears to be affected by the Woodworking skill.

Stone and Stone Roof are affected by Mining skill for now, it seems. Also, Stone Roof requires a bit more time than Stone.

When applying the patch, the server's serialization system detects a change and wipes the world:

[14:33 Eco.Plugin] Initializing Serialization...
[14:40 Eco.Plugin] Serialization version hash: B2E33DBA
[14:40 Eco.Plugin] Serialization change detected. Deleting storage...

Keeping the new version.eco file while reverting other files in the Storage folder causes some errors (see below), nullifying character progress and inventory. The world objects are gone too, with the error as reported above by Ryve.

...
[11:05 Eco.Plugin] 1 Error(s) occurred when loading laws:
Index was outside the bounds of the array.
...
[11:09 Eco.Plugin] 2 Error(s) occurred when loading users:
Invalid integer value in the input stream.
Invalid integer value in the input stream.
...
[11:05 Eco.Plugin] 1 Error(s) occurred when loading laws:
Index was outside the bounds of the array.

I think the population graph does include the dead bodies, because I've had the same problem, a lot of dead bodies laying around and then suddenly the next day a big population loss spike for all animals. I also had the same problem with animals running in one spot, not being able to move, even when shot at - probably the reason for not being able to reach the food sources. I haven't noticed any animal reproduction yet either.

I had problems with accessing the laws interface too, I had to run the server as admin to get it running locally and had to disable Windows 10 firewall for my external address, as adding the server.exe file to the exceptions did not have any effect.

Try looking for it higher up in mountainous areas. I've found veins with over 100 gold blocks in each of them in mountainous areas.

This has been reported as a bug already

Yes, the brown blotches are actually a growth state for Cabas bulbs and Bunchgrass, it is not a withered plant. It is quite confusing, yes. The plants take quite some time (around half a day?) to become fully grown, according to my experience.