diff --git a/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/projectmodel/tests/CProjectDescriptionSerializationTests.java b/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/projectmodel/tests/CProjectDescriptionSerializationTests.java
index f7d2fb39c40..dbe9223c266 100644
--- a/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/projectmodel/tests/CProjectDescriptionSerializationTests.java
+++ b/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/projectmodel/tests/CProjectDescriptionSerializationTests.java
@@ -172,6 +172,7 @@ public class CProjectDescriptionSerializationTests extends TestCase {
 			// Create model project and accompanied descriptions
 			IProject project = BuildSystemTestHelper.createProject(projectName);
 			ICProjectDescription des = coreModel.createProjectDescription(project, false);
+			des.setConfigurationRelations(ICProjectDescription.CONFIGS_INDEPENDENT);
 			Assert.assertNotNull("createDescription returned null!", des);
 
 			{
diff --git a/core/org.eclipse.cdt.core.tests/model/org/eclipse/cdt/core/settings/model/CProjectDescriptionDeltaTests.java b/core/org.eclipse.cdt.core.tests/model/org/eclipse/cdt/core/settings/model/CProjectDescriptionDeltaTests.java
index 3b864e88416..c6ff685dfa3 100644
--- a/core/org.eclipse.cdt.core.tests/model/org/eclipse/cdt/core/settings/model/CProjectDescriptionDeltaTests.java
+++ b/core/org.eclipse.cdt.core.tests/model/org/eclipse/cdt/core/settings/model/CProjectDescriptionDeltaTests.java
@@ -971,6 +971,8 @@ public class CProjectDescriptionDeltaTests extends BaseTestCase {
 		assertNotNull(prjDescription);
 		assertEquals(2, prjDescription.getConfigurations().length);
 
+		prjDescription.setConfigurationRelations(ICProjectDescription.CONFIGS_INDEPENDENT);
+
 		ICConfigurationDescription cfgDescription0 = prjDescription.getConfigurations()[0];
 		assertNotNull(cfgDescription0);
 		assertSame(cfgDescription0, prjDescription.getDefaultSettingConfiguration());
diff --git a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionPreferences.java b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionPreferences.java
index c7d4ff4cd5e..ee8e4cd124d 100644
--- a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionPreferences.java
+++ b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionPreferences.java
@@ -13,14 +13,19 @@
  *******************************************************************************/
 package org.eclipse.cdt.internal.core.settings.model;
 
+import org.eclipse.cdt.core.CCorePlugin;
 import org.eclipse.cdt.core.settings.model.ICProjectDescriptionPreferences;
 import org.eclipse.cdt.core.settings.model.ICStorageElement;
 import org.eclipse.cdt.core.settings.model.util.CDataUtil;
+import org.eclipse.core.runtime.preferences.DefaultScope;
 
 public class CProjectDescriptionPreferences implements ICProjectDescriptionPreferences {
+
 	private static final String ATTR_CONFIG_RELATIONS = "configRelations"; //$NON-NLS-1$
 
-	private static final int DEFAULT_RELATIONS = CONFIGS_INDEPENDENT;
+	// This preference is only used at Default Scope to allow product preference customization (plugin_customization.ini)
+	private static final String PREF_CPROJECTDESCRIPTION_CONFIG_RELATIONS_KEY = "cprojectdescription.configRelations"; //$NON-NLS-1$
+
 	private boolean fIsReadOnly;
 	private boolean fIsModified;
 
@@ -43,7 +48,8 @@ public class CProjectDescriptionPreferences implements ICProjectDescriptionPrefe
 		fIsReadOnly = isReadOnly;
 		if (el != null) {
 			if (el.getAttribute(ATTR_CONFIG_RELATIONS) != null)
-				fConfigRelations = Integer.valueOf(CDataUtil.getInteger(el, ATTR_CONFIG_RELATIONS, DEFAULT_RELATIONS));
+				fConfigRelations = Integer
+						.valueOf(CDataUtil.getInteger(el, ATTR_CONFIG_RELATIONS, getDefaultRelations()));
 		}
 
 		this.fSuperPreference = superPreference;
@@ -61,6 +67,11 @@ public class CProjectDescriptionPreferences implements ICProjectDescriptionPrefe
 			CDataUtil.setInteger(el, ATTR_CONFIG_RELATIONS, fConfigRelations.intValue());
 	}
 
+	public static int getDefaultRelations() {
+		return DefaultScope.INSTANCE.getNode(CCorePlugin.PLUGIN_ID)
+				.getInt(PREF_CPROJECTDESCRIPTION_CONFIG_RELATIONS_KEY, CONFIGS_LINK_SETTINGS_AND_ACTIVE);
+	}
+
 	@Override
 	public int getConfigurationRelations() {
 		if (fConfigRelations != null)
@@ -68,7 +79,7 @@ public class CProjectDescriptionPreferences implements ICProjectDescriptionPrefe
 		CProjectDescriptionPreferences superPrefs = getSuperPreferences();
 		if (superPrefs != null)
 			return superPrefs.getConfigurationRelations();
-		return DEFAULT_RELATIONS;
+		return getDefaultRelations();
 	}
 
 	@Override
diff --git a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/preferences/IndexerStrategyBlock.java b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/preferences/IndexerStrategyBlock.java
index a076dafdb8f..3f7b8894bba 100644
--- a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/preferences/IndexerStrategyBlock.java
+++ b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/preferences/IndexerStrategyBlock.java
@@ -18,6 +18,7 @@ import org.eclipse.cdt.core.settings.model.ICProjectDescriptionManager;
 import org.eclipse.cdt.core.settings.model.ICProjectDescriptionPreferences;
 import org.eclipse.cdt.core.settings.model.ICProjectDescriptionWorkspacePreferences;
 import org.eclipse.cdt.internal.core.pdom.indexer.IndexerPreferences;
+import org.eclipse.cdt.internal.core.settings.model.CProjectDescriptionPreferences;
 import org.eclipse.cdt.ui.dialogs.AbstractCOptionPage;
 import org.eclipse.cdt.ui.dialogs.ICOptionContainer;
 import org.eclipse.cdt.utils.ui.controls.ControlFactory;
@@ -143,8 +144,10 @@ public class IndexerStrategyBlock extends AbstractCOptionPage {
 	public void performDefaults() {
 		initUpdatePolicy(IndexerPreferences.getDefaultUpdatePolicy());
 		if (fUseActiveBuildButton != null) {
-			fUseActiveBuildButton.setSelection(false);
-			fUseFixedBuildConfig.setSelection(true);
+			boolean defaultUseActive = CProjectDescriptionPreferences
+					.getDefaultRelations() == ICProjectDescriptionPreferences.CONFIGS_LINK_SETTINGS_AND_ACTIVE;
+			fUseActiveBuildButton.setSelection(defaultUseActive);
+			fUseFixedBuildConfig.setSelection(!defaultUseActive);
 		}
 		updateEnablement();
 	}