Took me about two days testing theories to figure this out: If your ships are idle in the harbor and not transporting goods to islands, it's because you've built too many ships. Only build three (four maybe, but you'll be pushing your luck) and they don't seem to get confused, also try to build one harbor per island. This was so frustrating so I figured I'd share since no one seems to have figured this out on the net; I searched and searched unveiling people saying it's a game breaking bug.