diff --git a/bin/dunecontrol b/bin/dunecontrol
index 2b72260637fc57d972d50636a9a0a99444109f21..18561ba443201ca263ea255ac04f4335088a0856 100755
--- a/bin/dunecontrol
+++ b/bin/dunecontrol
@@ -346,7 +346,8 @@ run_default_autogen () {
   local M4_PATH=""
   if test -f configure.ac && \
      ( test -d .svn || test -d .git || test -d CVS || test -f stamp-vc ); then
-    for m in $FOUND_MODULES; do
+    sort_modules $FOUND_MODULES
+    for m in $MODULES; do
       path=$(eval "echo \$PATH_$m")
       MODULE_PATHS="$MODULE_PATHS$path "
     done