I can confirm that the duplicate header problem in WP 4.0 is due to the duplicate readme.txt files. Delete the one in the trunk and the plugin will activate.
You wouldn’t happen to be using a bridge would you? Are you using the WP users or pulling users from a forum?
The error “Are you sure you want to do this?” is because the nonce is not being verified (wp_verify_nonce). I’ve seen this in sites using third party bridges between forums and WordPress.
Are you using WP 3.5? I don’t even get the popup. Clicking on the green plus does not do anything.
