When changing the config for a server it seems to not be registering the changes properly. 1.18.2 is the version I am playing on. The config works perfectly as normal in Single-player worlds, but when transferred to the servers mod configs, it doesn't seem to make the appropriate change. The change I am referring to is to blockEntityEffect and the randomTickEffect for Crops/Livestock as well as furnaces and such. Any ideas on what I could be doing wrong, or is this a bug?

Did you change the multiplayer config? It's in different location than the single player one

Single-player worlds: ./saves//serverconfig/hourglass-server.toml
Multiplayer servers: ./world/serverconfig/hourglass-server.toml

And if those don't work, you can always use the /hourglass config command to change the settings

Yeah @yukkun had some good suggestions. Unfortunately I was not able to replicate the issues you are having (and not from a lack of trying). If you figure out a set of repeatable instructions I can take to reproduce the issue let me know.

Until then I am going to close this issue.