Maybe its time to apply some "Kentucky Windage"?
Lead the target maybe...?
Whenever my shells fall forward or aft? Of a vessel I just adjust fire till I score hits. In other words aim at the open sea and if the shell hits ..fire for effect.
But I have had the issue with my shells falling aft or forward of a target. It varies from near misses to the extreme. This does not occurr with every gun engagement for me though.
Possibly its the speed that the ships are travelling at, plus the distance. Maybe change you reload time witn commander and use rapid fire to adjust your aim easier?