diff --git a/build/org.eclipse.cdt.make.core/src/org/eclipse/cdt/make/internal/core/scannerconfig/gnu/ScannerInfoConsoleParserUtility.java b/build/org.eclipse.cdt.make.core/src/org/eclipse/cdt/make/internal/core/scannerconfig/gnu/ScannerInfoConsoleParserUtility.java
index 1ff5e0f1e53..af58dd60d6a 100644
--- a/build/org.eclipse.cdt.make.core/src/org/eclipse/cdt/make/internal/core/scannerconfig/gnu/ScannerInfoConsoleParserUtility.java
+++ b/build/org.eclipse.cdt.make.core/src/org/eclipse/cdt/make/internal/core/scannerconfig/gnu/ScannerInfoConsoleParserUtility.java
@@ -221,7 +221,7 @@ public class ScannerInfoConsoleParserUtility extends AbstractGCCBOPConsoleParser
 					// appending fileName to cwd should yield file path
 					filePath = cwd.append(fileName);
 				}
-				if (!filePath.toString().equalsIgnoreCase(EFSExtensionManager.getDefault().getPathFromURI(file.getLocationURI()))) {
+				if (!filePath.toOSString().equalsIgnoreCase(EFSExtensionManager.getDefault().getPathFromURI(file.getLocationURI()))) {
 					// must be the cwd is wrong
 					// check if file name starts with ".."
 					if (fileName.startsWith("..")) {	//$NON-NLS-1$
diff --git a/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/EFSExtensionProvider.java b/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/EFSExtensionProvider.java
index 10053b70211..7e8712bfe2f 100644
--- a/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/EFSExtensionProvider.java
+++ b/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/EFSExtensionProvider.java
@@ -10,6 +10,7 @@
  *******************************************************************************/
 package org.eclipse.cdt.core;
 
+import java.io.File;
 import java.net.URI;
 import java.net.URISyntaxException;
 
@@ -54,7 +55,7 @@ public abstract class EFSExtensionProvider {
 	 *         physical file.
 	 */
 	public String getPathFromURI(URI locationURI) {
-		return locationURI.getPath();
+		return new File(locationURI).getAbsolutePath();
 	}
 
 	/**