Index: src/config.h
===================================================================
RCS file: /cygdrive/d/cvs_doxygen/doxygen/doxygen/src/config.h,v
retrieving revision 1.6
diff -u -r1.6 config.h
--- src/config.h	12 May 2013 15:34:52 -0000	1.6
+++ src/config.h	20 May 2013 15:29:18 -0000
@@ -22,6 +22,7 @@
 #include <qstrlist.h>
 #include <qdict.h>
 #include <qlist.h>
+#include <qregexp.h>
 #include "ftextstream.h"
 
 
@@ -626,7 +627,7 @@
     {
       QCString result=m_userComment;
       m_userComment.resize(0);
-      return result;
+      return result.replace(QRegExp( "\r" ), "");
     }
 
   protected:
Index: src/config.l
===================================================================
RCS file: /cygdrive/d/cvs_doxygen/doxygen/doxygen/src/config.l,v
retrieving revision 1.9
diff -u -r1.9 config.l
--- src/config.l	19 May 2013 18:39:37 -0000	1.9
+++ src/config.l	20 May 2013 15:35:17 -0000
@@ -849,7 +849,7 @@
   if (m_userComment)
   {
     t << "\n";
-    t << m_userComment;
+    t << takeUserComment();
   }
 }
 
