There may be a little lag induced by the game as well.If you happen to bump any other command (rudder one way or the other, battle stations, speed increase/decrease) the "go to periscope depth" command seems forgotten. There have been several instances where I've had to re-apply that command, or manually set my depth to get the boat to begin diving.
Of course it could be because I didn't 'click' quite as thoroughly as I had intended.
Still, it's quite irritating to have the deck watch reporting an incoming plane well after those men should be closing the hatches.