No problem, glad I could help! I've actually never tried F5 with patch 1.2, I use voice command for manning the deck gun. As far as I can tell, it works properly. I've read that F5 actually man's the deck gun AND calls "Surface the boat" order, though if you order to man the deck gun I think you are already surfaced...
I have no idea why the patch changed that command the way it is now.