Configuration Files resetting with server restart

It seems that whenever I restart (or stop then start) the server all my configuration files are reset.
Is this necessary, is it a bug, is it known, and is it in the process of being fixed?

This bug makes it impossible for me to use my server correctly.

Basically what happens is whenever I go into a config file, I change something, restart my server for it to take effect and nothing happens because the config file remains untouched.
This is an issue that needs to be solved soon.

I am editing the config files while the server is running, but I can't see how that would cause an issue.

EDIT: I have tested this again, and it seems to only happen in the plugin 'SetSpawn'. This plugin would be unnecessary if EssentialsSpawn was added to the Plugins List, and so the issue would be resolved.

OK, I will try that Andreas. Thx. And I hit the save button, I am sure of that.

EDIT: Ok I think doing it while offline worked. Thx Andreas!