I’m not sure I fully understand the issue that is being described here.
Are you saying that when authenticated as the mentioned user, and calling /1.1/statuses/mentions_timeline.json, the specified Tweets do not show up?
This is difficult to debug as I don’t have user tokens for those accounts obviously, and some of them are now older Tweets that I would not expect to see in the response now.
I could speculate that this is a data center synchronisation and consistency issue, without understanding more about what you’re describing.