Philippe Virouleau introduced a bug about the scratchpad behaviour on the i3-discuss mailing list. I was able to reproduce it. This patch solves that problem.

To apply this patch, use:
curl http://cr.i3wm.org/patch/113/raw.patch | git am

@@ -1812,7 +1812,10 @@ void cmd_scratchpad_show(I3_CMD) {

     } else {

         TAILQ_FOREACH(current, &owindows, owindows) {

             DLOG("matching: %p / %s\n", current->con, current->con->name);

-            scratchpad_show(current->con);

+            /*The matched window should at least be floating.*/

+            if (current->con->floating >= FLOATING_AUTO_ON) {

+              scratchpad_show(current->con);

+            }

         }

     }