01-30-2015, 08:33 AM
That is unfortunately a bug that needs fixing. It happens because the server writes plugin-configurable values (i.e. EnableCommandBlocks) to file on server stop/restart, thus overwriting a previously changed value.
Meanwhile, you can try editing the value when the server is stopped, and then start it.
Meanwhile, you can try editing the value when the server is stopped, and then start it.