I also ran into an issue after updating to V2, even after removing SEG Classic completely and disabling the WWW Publishing Service before running the V2 installer.
The installation itself works fine, but on the Admin page for SEG V2 under ' Health' it says it can't get a connection to the mailserver.
I've double checked, in the config for V2 I use exactly the same URL for the mail server like in the config for SEG Classic, and there it works fine.
Apart from that everything shows green checkmarks on the Health page, API connectivity etc are fine.