diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/build/internal/core/scannerconfig/CfgScannerConfigUtil.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/build/internal/core/scannerconfig/CfgScannerConfigUtil.java
index 92f7a4e8a19..cc00ef236c5 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/build/internal/core/scannerconfig/CfgScannerConfigUtil.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/build/internal/core/scannerconfig/CfgScannerConfigUtil.java
@@ -22,6 +22,8 @@ import org.eclipse.cdt.managedbuilder.internal.core.ToolChain;
 
 public class CfgScannerConfigUtil {
 	public static CfgInfoContext adjustPerRcTypeContext(CfgInfoContext context){
+		if(((Configuration)context.getConfiguration()).isPreference())
+			return context;
         Tool tool = (Tool)context.getTool();
         IResourceInfo rcInfo = context.getResourceInfo();
         IInputType inType = context.getInputType();
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/build/internal/core/scannerconfig2/CfgScannerConfigInfoFactory2.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/build/internal/core/scannerconfig2/CfgScannerConfigInfoFactory2.java
index 084bb204577..27f064a305a 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/build/internal/core/scannerconfig2/CfgScannerConfigInfoFactory2.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/build/internal/core/scannerconfig2/CfgScannerConfigInfoFactory2.java
@@ -208,6 +208,8 @@ public class CfgScannerConfigInfoFactory2 {
 									}
 								}
 							} else {
+								if(cfg.isPreference())
+									continue;
 								CfgInfoContext context = new CfgInfoContext(rcInfo, tool, null);
 								context = CfgScannerConfigUtil.adjustPerRcTypeContext(context);
 								if(context != null && context.getResourceInfo() != null){
@@ -304,7 +306,7 @@ public class CfgScannerConfigInfoFactory2 {
 			if(!isPerRcTypeDiscovery())
 				return true;
 
-			return !CfgScannerConfigProfileManager.isPerFileProfile(profileId);
+			return CfgScannerConfigProfileManager.isPerFileProfile(profileId);
 		}
 	}
 
diff --git a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/DiscoveryTab.java b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/DiscoveryTab.java
index 1dc76782fb7..4bbf5ec15e0 100644
--- a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/DiscoveryTab.java
+++ b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/DiscoveryTab.java
@@ -311,40 +311,47 @@ public class DiscoveryTab extends AbstractCBuildPropertyTab implements IBuildInf
         int pos = 0;
         String savedId = buildInfo.getSelectedProfileId();
         ITool[] tools = null;
-		Tool tool = (Tool)iContext.getTool();
-		if(null == tool) {
-			IConfiguration conf = iContext.getConfiguration();
-			if(null != conf) {
-				tools = conf.getToolChain().getTools();
+        boolean needPerRcProfile = cbi.isPerRcTypeDiscovery();
+		if(!page.isForPrefs()) {
+			Tool tool = (Tool)iContext.getTool();
+			if(null == tool) {
+				IConfiguration conf = iContext.getConfiguration();
+				if(null != conf) {
+					tools = conf.getToolChain().getTools();
+				}
+				if(null == tools)
+					return;
 			}
-			if(null == tools)
-				return;
+			else
+				tools = new ITool[] { tool };
 		}
-		else
-			tools = new ITool[] { tool };
-        
         for (String profileId : profilesList) {
-    		boolean ok = false;
-        	for(int i = 0; i < tools.length; ++i) {
-        		IInputType[] inputTypes = ((Tool)tools[i]).getAllInputTypes();
-	        	if(null != inputTypes) {
-		        	for(IInputType it : inputTypes) {
-		        		String[] requiedProfiles = getDiscoveryProfileIds(tools[i], it);
-		        		if(null != requiedProfiles) {
-		        			for(String requiredProfile : requiedProfiles) {
-				        		if(profileId.equals(requiredProfile)) {
-				        			ok = true;
-				        			break;
-				        		}
-		        			}
-		        		}
+        	if(tools != null) {
+	    		boolean ok = false;
+	        	for(int i = 0; i < tools.length; ++i) {
+	        		IInputType[] inputTypes = ((Tool)tools[i]).getAllInputTypes();
+		        	if(null != inputTypes) {
+			        	for(IInputType it : inputTypes) {
+			        		String[] requiedProfiles = getDiscoveryProfileIds(tools[i], it);
+			        		if(null != requiedProfiles) {
+			        			for(String requiredProfile : requiedProfiles) {
+					        		if(profileId.equals(requiredProfile)) {
+					        			ok = true;
+					        			break;
+					        		}
+			        			}
+			        		}
+			        	}
 		        	}
+		        	if(ok)
+		        		break;
 	        	}
-	        	if(ok)
-	        		break;
-        	}
-        	if(!ok)
-        		continue;
+	        	if (!ok)
+	        		continue;
+        	} 
+    		if (needPerRcProfile && !CfgScannerConfigProfileManager.isPerFileProfile(profileId))
+    			continue;
+        
  			visibleProfilesList.add(profileId);
             labels[counter] = profiles[counter] = getProfileName(profileId);
             if (profileId.equals(savedId))