We are running
Bukkit-1.4.6-R0.3
world-edit version 5.4.6-tempfix2 (14-baf03a)
multiworld 4.4.2
and the latest Ports version on our server. The problem is, that a port created in one world is also found in the others and will port the player to the destination set for the created port.

Thanks very much for the report. This should be fixed in v0.3.2, pending approval on BukkitDev.

Thank you very much for your quick answer.
Is it possible to download a development-build of this newer version somewhere to try? Ports is the only plugin allowing our users to port, we do not use /warp, /tp and other commands and highly depend on it.
Thank you very much in advance for your answer.

Sure thing, here you go: http://robinjam.net/Ports.jar

Let me know if you have any other problems.

Thank you very much again. You're speed of answering is amazing :)
We'll let you know if there are other problems occuring.

EDIT: Issue is fixed. Thank you so much.