GroupManager Groups and perms work in all worlds, how do I stop this?

This can be fixed by editing your Group Manager configuration settings. Navigate to config.yml in your plugin/GroupManager/ directory.

In the mirrors section, you can setup configuration for all_unnamed_worlds. Any new worlds that get generated by the Multiverse plugin will fall under this category until otherwise specified.

Here's the annotated version of this configuration section in the documentation:

mirrors:
        # Worlds listed here have their settings mirrored in their children.
        # The first element 'world' is the main worlds name, and is the parent world.
        # subsequent elements 'world_nether' and 'world_the_end' are worlds which will use
        # the same user/groups files as the parent.
        # the element 'all_unnamed_worlds' specifies all worlds that aren't listed, and automatically mirrors them to it's parent.
        # Each child world can be configured to mirror the 'groups', 'users' or both files from its parent.
        world:
          world_nether:
          - users
          - groups
          world_the_end:
          - users
          - groups
          all_unnamed_worlds:
          - users
          - groups
    #  world2:      (World2 would have it's own set of user and groups files)
    #    world3:
    #    - users    (World3 would use the users.yml from world2, but it's own groups.yml)
    #    world4:
    #    - groups   (World4 would use the groups.yml from world2, but it's own users.yml)
    #  world5:
    #    - world6   (this would cause world6 to mirror both files from world5)

So you can either have all your new worlds inherit the groups.yml and users.yml from another world or define their own unique configurations entirely. This is really up to you how this is done.

Hope this helps!