If player logout on ship, plugin generate player clone on destination ship.
It can be used for cloning items.

bukkit 1.2.5
Ports 0.1.3

I'm going to close this issue since I was unable to reproduce it. If you are still having problems, feel free to re-open it and provide some more details.

What other plugins do you have installed? I can't think of anything that might be causing this issue other than a plugin conflict.