diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Tool.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Tool.java
index 93b00d76f6b..1d8e5d8c742 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Tool.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Tool.java
@@ -9,6 +9,7 @@
  *     IBM - Initial API and implementation
  *     Baltasar Belyavsky (Texas Instruments) - [279633] Custom option command-generator support
  *     Miwako Tokugawa (Intel Corporation) - bug 222817 (OptionCategoryApplicability)
+ *     Liviu Ionescu - [322168]
  *******************************************************************************/
 package org.eclipse.cdt.managedbuilder.internal.core;
 
@@ -4047,6 +4048,7 @@ public class Tool extends HoldsOptions implements ITool, IOptionCategory, IMatch
 				// find matching option
 				try {
 					if (op1.getValueType() == op2.getValueType() &&
+						op1.getName() != null &&
 						op1.getName().equals(op2.getName())) {
 						Object ob1 = op1.getValue();
 						Object ob2 = op2.getValue();
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/makegen/gnu/GnuMakefileGenerator.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/makegen/gnu/GnuMakefileGenerator.java
index 8c275d9924a..8f3d7effdb0 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/makegen/gnu/GnuMakefileGenerator.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/makegen/gnu/GnuMakefileGenerator.java
@@ -12,6 +12,7 @@
  *     Anna Dushistova  (Mentor Graphics) - [307244] extend visibility of fields in GnuMakefileGenerator
  *     James Blackburn (Broadcom Corp.)
  *     Marc-Andre Laperle
+ *     Liviu Ionescu - [322168] 
  *******************************************************************************/
 package org.eclipse.cdt.managedbuilder.makegen.gnu;
 
@@ -4013,7 +4014,12 @@ public class GnuMakefileGenerator implements IManagedBuilderMakefileGenerator2 {
 				Set<Entry<String, List<IPath>>> set = buildOutVars.entrySet();
 				for (Entry<String, List<IPath>> entry : set) {
 					String macroName = entry.getKey();
-					addMacroAdditionPrefix(map, macroName, "", false);	//$NON-NLS-1$
+					
+					// for projects with specific setting on folders/files do
+					// not clear the macro value on subsequent passes
+					if (!map.containsKey(macroName)) {
+						addMacroAdditionPrefix(map, macroName, "", false);	//$NON-NLS-1$
+					}
 				}
 
 				// Set of input extensions for which macros have been created so far