Had exactly the same problem as mentioned by the OP. To repeat:
1. User creates account.
2. Clicks on Activation Link in email.
3. Gets taken to a page that says Activation Successful. You can now Log in
4. Logs in (login is successful) but is taken to a page with a message, “Please enter a valid activation Key” with an empty field below.
5. If the user ignores this, he/she can start using all the BP features.
6. This message appears only the first time they log in. Doesn’t appear on future logins.
Have upgraded to the latest WP 3.1.3 and BP 1.2.8 and yet the problems persists. Any ideas.