This issue is rather odd. I have some scripts that do not work 100% right on servers unless I use /mt reload, but now as of late, I cannot use that command without encountering an error stating a fatal error has occurred. The server is running thermos, and if needed, I could run it on a vanilla server with these mods and scripts to see if I have the same issue. I don't know the specifics of the issue, but it appears to have started after I created some scripts related to Thaumcraft. I will list my script folder, which is kind of a mess, to see if anything stands out. The issue also causes some stuff like the disappearance of two of my custom thaumcraft pages upon the usage of /mt reload in a server.

Note: The server is also being hosted on another machine, and I have to remote to it. The scripts work fine in singleplayer.

Note 2: Some foreign commands might be the result of me using AMTweaker, to change AppleMilkTea's recipes to play better with Growthcraft.

https://www.dropbox.com/s/ped84smejbb5glu/scripts.zip?dl=0

Closing as I think I know the cause.