This same thing happened to me when I was on the Peninsula. There are two exits to the World Map there, and after visiting Sedona I walked east to all the trees, then took the northern trail to the World Map. My ship was there but when I tried to board, it kept moving away from me just like yours is doing. I re-entered the Peninsula and walked back down through the trees until I came to a trail heading east. It led to the other World Map exit and there was my ship again! This time I was able to board normally and problem was solved. I realized this was the dock where I'd actually left it in the first place, not the northern one. Why it showed up in the north as a mirage I have no idea -- must be a glitch. But maybe you're also at the wrong dock, and should look around for another exit to the World Map to find where you left your ship. Then you should be able to board and sail away. Good luck!
Edited on 11/06/2009 at 7:50:01 AM PST