Hi,
It turns out that the plugin will not correctly create links for subdirectory installations. This is a bug, will be fixed in the next release.
A possible work-around is to configure complete urls in the Page Links settings. F.ex. for your register page, set it to https://www.subdirectory.example.com/register or whatever the url is. Tip is copy the actual url from your browser to make it right.
I’m not sure what the issue is regarding the e-mail. Will plugin not send email what so ever, or is the verification link wrong/not working? Please give some more details.
The work-around given was for subdomain, but works for subdirectories too.
Regarding the problem with plugin not sending mails, one potential cause can be your Sender/replay address given in settings does not have a real e-mail account, but an e-mail alias. Some servers require sender’s from address must have an e-mail account.
Work-around can be to leave this field unset. In that case WordPress’ own settings will be used.