this is touched on in the FAQ
Its how WordPress does things for users.
If you think of from WPs view point .. when users are registered on a site from a Network they are known by the whole network. WP has one list of users for a Network, Multi-Network or single WP installation.
NSUR simply opens up the possibilities for limiting/allowing the sub-sites for users to register through. So with NSUR once a user is registered on a sub-site they are known to the whole Network (which is standard WP). The issues comes (as you have seen) that any user trying to register on a second sub-site will get the warning because they are bumping into themselves, or a previous account they created on the Network. If they approached the new sub-site having already logged into the network (through their account made available from their first registration) then NSUR will auto register them with the new sub-site once they enter the admin side.
the weakness is that the user may get confused if they are unaware that the second site is connected to a site they have already registered on. If you have different domain names for the sub-sites then it could lead to confusion. One way to get round this is to have a separate Network on the WP installation for each primary domain, you’ll then be moving into the world of multi-network WP installations which wp-multi-network is a great help for.
(Note there’s been no testing with “WP User Manager” and I’ve not heard of any conflicts)