Yes, shelling out of the game can and does cause inexplicable issues. From graphics anomalies all the way to CTDs. Just be sure that you have the correct tubes selected, and as RR points out, hit your "send" buttons twice. I will still every once in a while, send the torps off to points unknown, just by little mistakes. To hit a different spot on a ship, I usually use the middle angle deflection dial. Of course, that can contribute to wild misses ahead and behind...
