I'm pretty sure you could sail three tiles if they went fort>city>fortFirst, make sure you're playing Beyond the Sword; in previous versions of the game ships could not enter forts.
Second, forts and cities can form canals that ships can sail through, but the length of a canal can be no more than 2 tiles--so two forts or a fort and a city, that's it. Maybe you sailed through two forts and found you couldn't sail into the city that constituted the third tile.
but you could never sail two tiles that went fort>fort
regardless, I am unable to sail fort>city now so something has clearly changed.
Here is a picture of what is NOT working
Spoiler :
here is a picture of the exact same thing, only a couple years ago and it is working
Spoiler :

Here is the save file of the non-working canal, if anybody is curious.http://bespin.org/~papakapp/Civiv/asd;lkg AD-1979.CivBeyondSwordSave