Here I am to revive the thread.
I'm using Host Havoc for a server as well, and it seems that NONE of my Server Config settings are reflected in the final product. Whatever I put in on the Server isn't what's in the game.
Set a grace period for a few in-game days? Nope. Enemies swarmed us on night one.
Increased tool durability and mining speed? Nope.
Among a few other options, I don't think anything was set to what I had it set to be. I've fixed that by just using the /worldconfig commands when in game and altering the settings that I'm able to from there.
Average Host Havoc moment I guess.