I'm using Multiverse-NetherPortals build 529 with craftbukkit-1.2.5-R1.0. When you load it the first time it gets a severe error because is isn't creating the config.yml file correctly.

debug.log says
2012-04-17 23:41:15 [SEVERE] [MultiVerse-NetherPortals] Could not load config.yml

config.yml only says
worlds: {}

I manually modified the config.yml to match https://github.com/Multiverse/Multiverse-NetherPortals/wiki/config.yml and then the plugin works.

Should be fine in latest versions: http://multiverse.github.com/news/better-end-support.html