Are you using multisite?
Multisite runs differently than single site (standard) WordPress. All users are network users and are then enabled for individual sites. So an administrator of a site in multisite does not have the ability to edit users (which is what they need to be able to activate users) unless they are a super administrator (admin at the network level).
Yes, I’m running multisite, but your plugin isn’t network activated. I can not provide Super Admin access to the secondary user.
but your plugin isn’t network activated.
It’s not really a matter of whether it’s network activated or not. It’s a matter of user capability.
In order to activate a user, the user activating that user must have the ‘edit_users’ capability assigned to the role. In multisite, the only role that has edit_users as a capability is the super admin role (as explained above).