The patch from bug 709085 has a bug in the strip_xkb_option function, which causes it to sometimes keep some of the prefixed options in the list. Here's a trivial (and untested!) patch:

diff --git a/plugins/keyboard/gsd-keyboard-manager.c b/plugins/keyboard/gsd-keyboard-manager.c
index 7e876fe..d8ff930 100644
--- a/plugins/keyboard/gsd-keyboard-manager.c
+++ b/plugins/keyboard/gsd-keyboard-manager.c
@@ -875,8 +875,9 @@ strip_xkb_option (gchar       **options,
                         g_free (*p);
                         *p = options[last];
                         options[last] = NULL;
+                } else {
+                        p += 1;
                 }
-                p += 1;
         }
 }