Fix packetbeat flaky tests (elastic#5200)

Moved the shutdown timeout after stopping the flows, but before stopping
the transaction publishing. It needs to be after stopping the flows because
the tests rely on the shutdown sequence to create flow reports.

(cherry picked from commit c0de062)

packetbeat/beater/packetbeat.go

@@ -177,6 +177,12 @@ func (pb *packetbeat) Run(b *beat.Beat) error {
 	}()
 
 	defer pb.transPub.Stop()
+
+	timeout := pb.config.ShutdownTimeout
+	if timeout > 0 {
+		defer time.Sleep(timeout)
+	}
+
 	if pb.flows != nil {
 		pb.flows.Start()
 		defer pb.flows.Stop()
@@ -204,11 +210,6 @@ func (pb *packetbeat) Run(b *beat.Beat) error {
 		return err
 	}
 
-	timeout := pb.config.ShutdownTimeout
-	if timeout > 0 {
-		time.Sleep(timeout)
-	}
-
 	return nil
 }