diff --git a/build/org.eclipse.cdt.make.core/src/org/eclipse/cdt/make/internal/core/scannerconfig/gnu/GCCPerFileBOPConsoleParser.java b/build/org.eclipse.cdt.make.core/src/org/eclipse/cdt/make/internal/core/scannerconfig/gnu/GCCPerFileBOPConsoleParser.java
index ef8aaf5cd91..d0f41db694d 100644
--- a/build/org.eclipse.cdt.make.core/src/org/eclipse/cdt/make/internal/core/scannerconfig/gnu/GCCPerFileBOPConsoleParser.java
+++ b/build/org.eclipse.cdt.make.core/src/org/eclipse/cdt/make/internal/core/scannerconfig/gnu/GCCPerFileBOPConsoleParser.java
@@ -121,7 +121,7 @@ public class GCCPerFileBOPConsoleParser extends AbstractGCCBOPConsoleParser {
             
             IFile file= null;
             IPath baseDirectory= fUtil.getBaseDirectory();
-            if (baseDirectory.isPrefixOf(pFilePath)) {
+            if (baseDirectory.isPrefixOf(pFilePath) || baseDirectory.setDevice(null).isPrefixOf(pFilePath)) {
 				IPath relPath = pFilePath.removeFirstSegments(baseDirectory.segmentCount());
 				//Note: We add the scanner-config even if the resource doesn't actually
 				//exist below this project (which may happen when reading existing