Merri: The seafaring AI in S2 is a bit sloppy. Back in the days the devs didn't get enough time to fix it until the deadline for expansion pack with a map editor, so they simply disabled harbors everywhere except in the campaign.
To get it to work you need to:
1. Only build one harbor per island / area.
2. Keep amount of ships low.
Despite these actions it may sometimes take a very long time for resources to move from A to B when going overseas, but at least they usually do if you "keep it simple".
Thanks for the response. Hopefully not too many similar problems during the rest of the campaign.
S.x.