diff --git a/src/main/java/net/knarcraft/stargate/Stargate.java b/src/main/java/net/knarcraft/stargate/Stargate.java
index e4ef6c1..0102695 100644
--- a/src/main/java/net/knarcraft/stargate/Stargate.java
+++ b/src/main/java/net/knarcraft/stargate/Stargate.java
@@ -25,6 +25,7 @@ import net.knarcraft.stargate.thread.BlockChangeThread;
 import net.knarcraft.stargate.thread.ChunkUnloadThread;
 import net.knarcraft.stargate.thread.StarGateThread;
 import net.knarcraft.stargate.utility.BStatsHelper;
+import org.bukkit.Bukkit;
 import org.bukkit.Server;
 import org.bukkit.command.PluginCommand;
 import org.bukkit.configuration.InvalidConfigurationException;
@@ -73,7 +74,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 @SuppressWarnings("unused")
 public class Stargate extends JavaPlugin {
 
-    private static File configFile;
+    private static final String configFileName = "config.yml";
     private static final Queue<BlockChangeRequest> blockChangeRequestQueue = new LinkedList<>();
     private static final Queue<ChunkUnloadRequest> chunkUnloadQueue = new PriorityQueue<>();
 
@@ -247,7 +248,14 @@ public class Stargate extends JavaPlugin {
      * @param message  <p>The message to log</p>
      */
     private static void log(Level severity, String message) {
-        logger.log(severity, getBackupString("prefix") + message);
+        if (logger == null) {
+            logger = Bukkit.getLogger();
+        }
+        if (getInstance() == null) {
+            logger.log(severity, "[Stargate]: " + message);
+        } else {
+            logger.log(severity, getBackupString("prefix") + message);
+        }
     }
 
     /**
@@ -349,9 +357,9 @@ public class Stargate extends JavaPlugin {
         super.reloadConfig();
         this.configuration = new StargateYamlConfiguration();
         try {
-            configuration.load(configFile);
+            configuration.load(new File(getDataFolder(), configFileName));
         } catch (IOException | InvalidConfigurationException e) {
-            Stargate.logSevere(e.getMessage());
+            e.printStackTrace();
         }
     }
 
@@ -359,9 +367,9 @@ public class Stargate extends JavaPlugin {
     public void saveConfig() {
         super.saveConfig();
         try {
-            configuration.save(configFile);
+            configuration.save(new File(getDataFolder(), configFileName));
         } catch (IOException e) {
-            logSevere(e.getMessage());
+            e.printStackTrace();
         }
     }
 
@@ -375,16 +383,16 @@ public class Stargate extends JavaPlugin {
 
     @Override
     public void onEnable() {
-        configFile = new File(this.getDataFolder(), "config.yml");
+        this.saveDefaultConfig();
+        this.getConfig();
         PluginDescriptionFile pluginDescriptionFile = this.getDescription();
         pluginManager = getServer().getPluginManager();
         configuration = new StargateYamlConfiguration();
         try {
-            configuration.load(configFile);
+            configuration.load(new File(getDataFolder(), configFileName));
         } catch (IOException | InvalidConfigurationException e) {
-            Stargate.logSevere(e.getMessage());
+            getLogger().log(Level.SEVERE, e.getMessage());
         }
-        this.saveDefaultConfig();
         configuration.options().copyDefaults(true);
 
         logger = Logger.getLogger("Minecraft");
diff --git a/src/main/java/net/knarcraft/stargate/config/StargateConfig.java b/src/main/java/net/knarcraft/stargate/config/StargateConfig.java
index ea8598d..a7aecf4 100644
--- a/src/main/java/net/knarcraft/stargate/config/StargateConfig.java
+++ b/src/main/java/net/knarcraft/stargate/config/StargateConfig.java
@@ -15,6 +15,7 @@ import org.bukkit.Bukkit;
 import org.bukkit.World;
 import org.bukkit.command.CommandSender;
 import org.bukkit.configuration.file.FileConfiguration;
+import org.bukkit.configuration.file.YamlConfiguration;
 import org.bukkit.plugin.messaging.Messenger;
 import org.dynmap.DynmapAPI;
 
@@ -434,18 +435,25 @@ public final class StargateConfig {
     /**
      * Changes all configuration values from the old name to the new name
      *
-     * @param newConfig <p>The config to read from and write to</p>
+     * @param currentConfiguration <p>The current config to back up</p>
      */
-    private void migrateConfig(FileConfiguration newConfig) {
+    private void migrateConfig(FileConfiguration currentConfiguration) {
         //Save the old config just in case something goes wrong
         try {
-            newConfig.save(dataFolderPath + "/config.yml.old");
+            currentConfiguration.save(new File(dataFolderPath, "config.yml.old"));
         } catch (IOException e) {
             Stargate.debug("Stargate::migrateConfig", "Unable to save old backup and do migration");
             e.printStackTrace();
             return;
         }
 
+        //Load old and new configuration
+        Stargate.getInstance().reloadConfig();
+        FileConfiguration oldConfiguration = Stargate.getInstance().getConfig();
+        YamlConfiguration newConfiguration = StargateYamlConfiguration.loadConfiguration(
+                FileHelper.getBufferedReaderFromInputStream(
+                        FileHelper.getInputStreamForInternalFile("/config.yml")));
+
         //Read all available config migrations
         Map<String, String> migrationFields;
         try {
@@ -460,15 +468,30 @@ public final class StargateConfig {
 
         //Replace old config names with the new ones
         for (String key : migrationFields.keySet()) {
-            if (newConfig.contains(key)) {
+            if (oldConfiguration.contains(key)) {
                 String newPath = migrationFields.get(key);
-                Object oldValue = newConfig.get(key);
+                Object oldValue = oldConfiguration.get(key);
                 if (!newPath.trim().isEmpty()) {
-                    newConfig.set(newPath, oldValue);
+                    oldConfiguration.set(newPath, oldValue);
                 }
-                newConfig.set(key, null);
+                oldConfiguration.set(key, null);
             }
         }
+
+        // Copy all keys to the new config
+        for (String key : oldConfiguration.getKeys(true)) {
+            Stargate.logInfo("Setting " + key + " to " + oldConfiguration.get(key));
+            newConfiguration.set(key, oldConfiguration.get(key));
+        }
+
+        try {
+            newConfiguration.save(new File(dataFolderPath, "config.yml"));
+        } catch (IOException e) {
+            Stargate.debug("Stargate::migrateConfig", "Unable to save migrated config");
+            e.printStackTrace();
+        }
+
+        Stargate.getInstance().reloadConfig();
     }
 
     /**
diff --git a/src/main/java/net/knarcraft/stargate/config/StargateYamlConfiguration.java b/src/main/java/net/knarcraft/stargate/config/StargateYamlConfiguration.java
index 2b5f751..4326f81 100644
--- a/src/main/java/net/knarcraft/stargate/config/StargateYamlConfiguration.java
+++ b/src/main/java/net/knarcraft/stargate/config/StargateYamlConfiguration.java
@@ -19,6 +19,12 @@ public class StargateYamlConfiguration extends YamlConfiguration {
     static public final String END_OF_COMMENT = "_endOfComment_";
     static public final String START_OF_COMMENT = "comment_";
 
+    @Override
+    @SuppressWarnings("deprecation")
+    protected @NotNull String buildHeader() {
+        return "";
+    }
+
     @Override
     public @NotNull String saveToString() {
         return this.convertYAMLMappingsToComments(super.saveToString());