I am having a similar problem. The activation email sent is NOT the custimized email that I created. It appears to be the standard WP email; however, it lacks any activation links. My users are not able to activate!!!
PLEASE HELP!!
thesurfinstitute.com
Can you make your own topic in future please? These two issues may have different causes. You two are using BuddyPress, right? Are you running any translations for BuddyPress on your site?
Sorry for not making a new topic. I noticed mwbarker posted a month ago w/ a similar problem & hadn’t received a response yet. I thought I was helping him by bumping it up… 
I am using Buddypress 1.5.5, WordPress 3.3.1. Sorry, to seem dense… I’m a bit green to all this… unless you mean something other than literally translating into different languages, I am not.
An activation email is sent, but it is not customized and contains no activation link.
Are you using multisite, or have you set the BP_ROOT_BLOG setting anywhere?
What other plugins are you running?
Not running multisite nor have I done anything to the BP_ROOT_BLOG setting.
Plugins are (a bit numerous):
Ad Codes Widget
Akismet
Another WordPress Classifieds Plugin (AWPCP)
Basic Google Maps Placemarks
BuddyPress
BuddyPress Activity Plus
BuddyPress Group Email Subscription
BuddyPress Template Pack
CD BuddyPress Avatar Bubble
Custom Login lite
Dynamic Widgets
Easy iFrame Loader
eShop for WordPress
Favicon Rotator
Formidable
Formidable Payment
Global Hide/Remove Admin Bar Plugin
Lux Vimeo
Member Access
Ninja Pages, Categories, and Tags
Official StatCounter Plugin
Online Backup for WordPress
Portfolio Slideshow Pro
SI CAPTCHA Anti-Spam
Sidebar Login
Simple Google Analytics
Trackable Social Share Icons
User Role Editor
Welcome Pack
Wordpress Font Uploader
WP-Mail-SMTP
WP Issuu
WPMU DEV Update Notifications
WP Show IDs
WP Sliding Login | Register Panel
WP Super Cache
I had Social Login, too, but deactivated it after reading that others found incompatibility with the two plugins.
I have discovered that NONE of my emails are showing my customizations. For instance, the “new friend request fro %s” email appears just as plain text.
So, I’ve made some changes, but still not receiving a link in the activation email. Email arrives, but it’s blank.
Deactivated: Welcome Pack & Member Access.
Installed: s2member (discovered certain pages were not being hidden by Member Access).
Installed: BuddyPress Pending Activation (With this I can now activate or resend an activation email – which comes in an entirely different format than the initial one and contains a working activation link)
I’d like to use Welcome Pack, but wasn’t sure if it was causing issues.
Sorry, thought I would get a notification on replies to this thread. I am running BuddyPress – no translation – no multi-site.
Just to let everyone know I am aware but haven’t looked at this yet.
