I had the same issue and I want to share here what I did to make activation emails reach the inbox (especially in Gmail):
– added SPF and DKIM DNS records in order to certify that the e-mails are legitimate, especially if your host uses a third party service to send them, or they get sent from a different domain
– changed the default “from” e-mail address and “from name” fields using a plugin. I used WP-Mail-SMTP plugin that also allows me to use my own e-mail address (like a google apps one), but there are plenty others that you could use
After these steps the e-mails were still being marked as spam by Gmail and the only thing left was to edit the activation e-mail content itslef. Thank you Paul for adding the option in Welcome Pack plugin. I enabled “Customise the emails sent by BuddyPress, either in plain text or rich HTML versions.” I then edited the content and subject by adding more text and there it was, activation e-mail wasn’t marked as spam anymore.
I hope this helps someone else as I spent quite some time making it work 🙂
