I am having a similar issue as above.
When the plugin is enabled the ‘set password’ link is missing from the email when I create a new user.
When I disable the plugin an add a user to my site they are emailed in plain text a link to set their own password.
If I do a password reset for that user, the link is also missing in that email too when the plugin is active.
I don’t have woocommerce or any member plugins active.