Fixed my fix (because Bukkit is stupid & durability counts up).

src/main/java/com/gmail/nossr50/skills/Excavation.java

@@ -206,7 +206,7 @@ public class Excavation
 			if(!player.getItemInHand().containsEnchantment(Enchantment.DURABILITY))
 			{
 				short durability = player.getItemInHand().getDurability();
-				durability -= LoadProperties.abilityDurabilityLoss;
+				durability += LoadProperties.abilityDurabilityLoss;
 				player.getItemInHand().setDurability(durability);
 			}
     	}

src/main/java/com/gmail/nossr50/skills/Mining.java

@@ -266,7 +266,7 @@ public class Mining
     		if(!player.getItemInHand().containsEnchantment(Enchantment.DURABILITY))
     		{
 				short durability = player.getItemInHand().getDurability();
-				durability -= LoadProperties.abilityDurabilityLoss;
+				durability += LoadProperties.abilityDurabilityLoss;
 				player.getItemInHand().setDurability(durability);
     		}
     	}

src/main/java/com/gmail/nossr50/skills/WoodCutting.java

@@ -263,13 +263,9 @@ public class WoodCutting
 	    {
 	    	if(!player.getItemInHand().containsEnchantment(Enchantment.DURABILITY))
 	    	{
-	    		System.out.println("BEFORE");
-	    		System.out.println(player.getItemInHand().getDurability());
 				short durability = player.getItemInHand().getDurability();
-				durability -= LoadProperties.abilityDurabilityLoss;
+				durability += LoadProperties.abilityDurabilityLoss;
 				player.getItemInHand().setDurability(durability);
-				System.out.println("AFTER");
-				System.out.println(player.getItemInHand().getDurability());
 	    	}
 	    }