Sometimes in BOS for the shuttle they'll just load whoever is in the gate area onto the plane, no matter what time their shuttle flight is for.

The Suttle agents are great and have always been much more willing to work with someone.

Since you're going to CLT, is there a direct flight you can get on? I'd go to the Elite check in line (or the shuttle check in line) and ask for a direct routing if possible - if there's seats maybe they'll do it.