It sounds like you need to add a function that automatically clears down all the notifications for that content when the content is viewed by the user. There’s nothing built into BP to do that.
If it was me I’d retrace the function that is producing that message and work back from it to find out what BP check is failing in order to understand what data BP is looking for, I’d then check the data stored in the DB to make sure it’s correct.
One thing you could try is to goto admin>>Tools>>BuddyPress and see if the DB fix tools supplied help.
The activition email that you are sending out has the link formatted exactly the same as I would expect. On my test system when I click that link it automatically populates the input box with the activation key, on your system is does not fill the input box and it needs to be manually pasted in place. Seems to point to something different about your activate.php file. I don’t suppose you’ve made changes to this, or maybe your theme has?
It’s worth trying deleting BuddyPress and reinstalling, but this seems more db related. Basically BuddyPress thinks your users do not have the right privileges to view their messages.
You might like to consider setting up a separate test system in order to better test your configurtion without messing with your live setup. It’s highly recommended for any critical WP install.
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