diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/BuildDescription.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/BuildDescription.java
index 8bff0c06021..dde1a0a9c4f 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/BuildDescription.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/BuildDescription.java
@@ -391,6 +391,9 @@ public class BuildDescription implements IBuildDescription {
 			DbgUtil.traceln("--->Synch started");	//$NON-NLS-1$
 
 		BuildDescriptionManager.accept(new RebuildStateSynchronizer(), this, true);
+		
+		if(fOutputStep.needsRebuild())
+			fInputStep.setRebuildState(true);//needed for the pre-build step invocation
 
 		if(DbgUtil.DEBUG)
 			DbgUtil.traceln("<---Synch stopped");	//$NON-NLS-1$
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/GenDirInfo.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/GenDirInfo.java
index 0c7ec2e950b..a4475267ef7 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/GenDirInfo.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/GenDirInfo.java
@@ -47,7 +47,7 @@ public class GenDirInfo {
 		if(path != null
 				&& fProjPath.isPrefixOf(path)){
 			path = path.removeLastSegments(1).removeFirstSegments(1);
-			if(fDirPathSet.add(path)){
+			if(path.segmentCount() > 0 && fDirPathSet.add(path)){
 				IFolder folder = fProject.getFolder(path);
 				if(!folder.exists()){
 					try {