If you walk through a nether portal you spawn at the correct location in the nether but no portal is generated or if there is already a portal in range it is not linked. Same bug appear in opposite direction Nether => normal world.

Everything works fine on the default map with the default nether.

I think this is a bukkit bug but I post it here because you have more information's how this plugin works and what the differences between the default world and extra worlds are.

Bukkit: CraftBukkit version git-Bukkit-1.4.7-R1.0-b2624jnks (MC: 1.4.7) (Implementing API version 1.4.7-R1.0)

Mulitverse: latest dev builds

#68 has more info and possible fixes.