diff --git a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/core/settings/model/util/SettingsSet.java b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/core/settings/model/util/SettingsSet.java
index c5dba340082..d9b1d99e9db 100644
--- a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/core/settings/model/util/SettingsSet.java
+++ b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/core/settings/model/util/SettingsSet.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2007 Intel Corporation and others.
+ * Copyright (c) 2007, 2008 Intel Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
@@ -319,9 +319,12 @@ public class SettingsSet {
 			EntryNameKey key = new EntryNameKey(entry);
 			Object[] o = (Object[])map.get(key);
 
+			
 			if(o != null && valueMatches(entry, o[1])){
 				mapCopy.remove(key);
 				levelInteger = (Integer)o[0];
+				if (! entry.isBuiltIn()) // allow overwrite existing entry,
+					levelInteger = null; // even with the same value
 			} else {
 				levelInteger = null;
 			}