@maguire ,
I haven't done any serious work with the custom gradebook columns (just testing things for people in the Community). Since they have to be added through the API, that means that no one else at our school has either, so I don't have any data to debug the situation with; sorry.
You're pretty on top of things, so I doubt either of these is the problem, but I'll mention them because I don't have anything else to offer.
For clarification, are you saying that the 5 that were found did not have any data in them? The documentation says that it only returns students who have associated data. Is it possible that you got the wrong column ID? Another question would be if you added the include_hidden query parameter? In getting both the list of columns and the data, it defaults to not showing hidden columns. Beyond that, I'm not going to be able to help out on this one.
Finally, you tagged the wrong James Jones. A trick I've learned when there are common names is to right click on the person's name from the header of a previous post and copy the link. Then paste it into the message and Jive will convert it to the person's name.