src/Pure/Build/build_job.scala

 
     private def nodes_status_progress(): Unit = {
       val state = get_state()
       val result =
         synchronized {
-          for (id <- state.progress_theories) nodes_changed += id
+          for (id <- state.progress_theories if !nodes_changed(id)) nodes_changed += id
           val nodes_status1 =
             nodes_changed.foldLeft(nodes_status)({ case (status, state_id) =>
               state.theory_snapshot(state_id, build_blobs) match {
                 case None => status
                 case Some(snapshot) =>