Certainly on BA, when someone checks in on a through connection to another airline but doesn't print the boarding pass, it is not immediately obvious to a check-in agent how to get a boarding pass for the onward flight. Very few agents would know that the way to do it, is to request a seat change on the onward flight, but put the same seat number the customer already has in the "new seat number" box. This will then print the boarding pass for the seat already checked in to.

All airlines use EDIFACT http://en.wikipedia.org/wiki/EDIFACT for checking in customers on flights operated by other airlines so I imagine the back end system is exactly the same, making it difficult for the check-in agent in MJV to print a boarding pass for you.