diff -urN doxygen-1.5.5/src/util.cpp doxygen-1.5.5.brokenpaths/src/util.cpp
--- doxygen-1.5.5/src/util.cpp	2008-01-19 16:54:27.000000000 +0100
+++ doxygen-1.5.5.brokenpaths/src/util.cpp	2008-03-14 16:45:47.000000000 +0100
@@ -4468,7 +4468,7 @@
       QCString pathStripped = stripFromIncludePath(path);
       for (fni.toFirst();(fd=fni.current());++fni)
       {
-        QCString fdStripPath = stripFromIncludePath(fd->getPath());
+        QCString fdStripPath = stripFromIncludePath(fd->getPath().right(path.length()));
         if (path.isEmpty() || fdStripPath==pathStripped) 
         { 
           count++;