Server Backups and Server never saves

I run a server with mods and whenever I try to use a backup when the server is up it doesnt do anything and when I shut off the server and then back it up it works, but when I back it up it doesnt backup what I was doing in the server it just backup the world when it was first created, so what Im trying to say is that whenever I try to save anything it never does not matter how much i reinstall the server or change somthing. Please help me.