Thanks all!
Unbelievably, I think that the problem was the 'ticking the final box' solution proposed by Theodulus. I am kicking myself

I have only managed to find a spare hour this weekend to even play the game, and the only ship I found was despatched by deck gun to save torpedos so still not had chance to try out the advice offered here. I'm sure I will meet with more success in future!
Regarding the mods, which comes recommended in terms of realism? I have looked into the Grey Wolves mod and that looks quite good, though I am worried as whenever I have tried installing mods for previous games it has gone horribly wrong for me, but with the help of you guys I am sure I will meet with more success this time!