Just upgraded from WP 3.9.2 to WP 4.3 multisite installation that also uses Pro Sites Version 3.5.1. We also have plugin "Unconfirmed" installed (https://wordpress.org/plugins/unconfirmed/). I did have some MU_plugins that tweaked some email message content, but have moved those to a mu-plugins-disabled folder for now
So ... everything is working (pretty much) as expected after upgrades, with the exception of account activation emails are not being sent when a new user signs up or when we use the "resend activation email" from within the Unconfirmed plugin. I have disabled the Unconfirmed plugin, and tried to sign up again as a new user. This sites are cued up and when I manually hit the activation URL at the subdomain site (i.e. https://subdomain.domain.com/wp-activate.php?key=f9741c1eefbb5a56 --- for example) the user and site activate as expected.
Password reset emails ARE being sent, notification of manually activated site emails ARE being sent ... BUT just not the activation emails. So I know mail is being sent as expected by the server.
Wondering if anyone else is experiencing this too? And any tips to solve the issue would be great. Yes, I have checked the server logs and there are no errors from my IP.