I believe Shanghaiceltic is very close. "Kissing the gunner's daughter" referred to the practice of tying the lad to the cannon, so that he could receive his beating. It might have looked a bit as if the lad were trying to make love to the cannon, which gave rise to the grim humour (not at all uncommon in the navy).
I can try to find a URL to a site with more on this subject later on.