Is there a specific permission that I am missing? Players read that the "ship will depart in x minutes" but when it gets to 0 nothing happens. What have I missed?

I'm going to close this issue since I was unable to reproduce it and it may have been fixed as a side-effect of other bugfixes. If you are still having problems, please feel free to re-open it.

I am not getting anything in the server log either, but I can use warps. I am oped, and I am trying it unoped right now.

They are both in the same world, but the world is not named world, it is named Skylands. It is also not the default world. Could this have an effect on that?

This is what comes up in the console when I launch.
23:13:39 [INFO] While loading Ports (plugins/ports.jar) found old-data folder: plugins/ports next to the new one: plugins/Ports
23:13:39 [SEVERE] ebean.properties not found
23:13:39 [INFO] DataSourcePool [Ports] autoCommit[false] transIsolation[SERIALIZABLE] min[2] max[20]
23:13:39 [INFO] SubClassFactory parent ClassLoader [org.bukkit.plugin.java.PluginClassLoader]
23:13:39 [INFO] Entities enhanced[0] subclassed[1]

Obviously an excerpt, but this is all that I found relevant that could possibly be a problem causer.

Also, should there be a config file? All that is in my ports folder is Ports.db I am using the latest dev build, if that makes any sort of difference. Thanks for your patience on this one. Also, I was able to use the port unoped, but other people can't. I deleted my ports folder and redownloaded the jar, I am waiting for someone to log in to test it for me.

Are the 2 ports in the same world? If they're in different worlds, you need to make sure the players have permission to change world (for example, the Multiverse permission node would be multiverse.access.WORLDNAME).

Sorry for the really late reply.

No, there currently isn't a config file (in older versions of Ports it would create a default config.yml file but do nothing with it). I can't think of any reason why it isn't working, but I'm currently making some big changes to the plugin that may or may not fix your problem - we'll have to wait and see :P