The server doesn't seem to load existing reputation values from villages.dat into it's runtime.
TreeMap "j" in Village.java stays empty despite existing data, Village being loaded in the world and related player having joined.

Additionally, saving the values in runtime to NBTTag is not reliable. It appears as if there was only a scheduler behind a(NBTTagCompound x). So if starting the server, generating a reputation value and stopping the server is done in a short timeframe, no change is made to the value.

Value was checked using NBTExplorer and after the server was stopped.