diff --git a/src/run_autoconfig b/src/run_autoconfig
index 0fed0b518af02fec8ed6576877cc846a3e82be04..c3986f7851fee2ee18d6771fdb67604ea72373a2 100755
--- a/src/run_autoconfig
+++ b/src/run_autoconfig
@@ -10,6 +10,12 @@ fix()
 
   if [ ! -f $1/Makefile.in ]; then
     cp $1/Makefile.src $1/Makefile.in
+  else if cmp $1/Makefile.src $1/Makefile.in >/dev/null; then
+    :
+  else
+    # This might not be strictly necessary, but you
+    # need to run 'make depend' afterwards anyway.
+    cp $1/Makfile.src $1/Makefile.in
   fi
 }