This has bothered me since I played an AD character in the beta. When you're done with the quests at Khenarthi's Roost, you finish up near Mistral (at Cat's Eye Quay). Many of the characters you've dealt with on the various quests were there for the final battle and are lined up to congratulate you, including Jimila, the captain of the Prowler, who was part of the Shattered Shoals quest. In fact, Jimila offers to ferry you to Auridon if you just hop in the launch.
If this is bugged for you, this is where the confusion set in. You don't get the message to use 'E' to enter the boat. Not realizing that you should have gotten it, if you're like me, you try to enter the boat. The boat behind her doesn't have a gangplank to walk over, so you have to carefully jump into it, and sometimes you'll see a whole group of people doing leap after leap into the water, trying to land on the boat.
But landing on the boat doesn't solve the problem, because she doesn't ferry you to Auridon, but just offers the same conversation topics you've already gone through.
Thanks to everyone who helped me finally figure out what was going on. Here is a map that shows where you are and where you need to be to actually find the "real" way back (without using the wayshrines).
Edited by Teeg on April 14, 2014 4:07PM
Mara's Tester
Psijic Order
Sidekick Order
Karma Chameleon
She Who Explores
She Who Wanders
Te-ge
She Who Wonders (EU)
Mara's Moxie
The Sidekick Order
The Psijic Order