This is now solved The solution was this in the activation script:
$blog_real_id = $wpdb->get_var("select blog_id from wp_bp_user_blogs where user_id = ".$user_id." limit 1");
wp_cache_key_delete("1:users:".$user_id);
wp_cache_key_delete($blog_real_id.":users:".$user_id);
This clears the cached user info for blog id 1 and the signed up blog ud. For some reason the password hash that is in memcache is wrong. Clearing it before logging in will authenticate aginst mysql insterad of the cached password in memcache.
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