I've been working with References at work a lot lately and, if the issue isn't as Wes described, I think
I know what's happening in your scene:
Check the Fill Channel for the reference that's refusing to update. If you hover over it, does it say 'Channel Not Referenced?' If so, right-click over the channel icon and sync it manually. After that, the channel should Update when you use the Update Reference command. (Wes helped me figure that one out.) If that doesn't work, it's probably what he said in the above post.
If what I described does work for you, here's what little I know about the issue:
For some reason, when I'm working with references, some of the referenced layers and referenced imports may get these randomly activated channels. When they appear, these channels are typically not in use by the source file or layer so they appear benign. But if we happen to keyframe them in the source file or layer after the scene has been distributed to other artists for animation, these 'mystery keys' can block the Update command for those channels. It's very annoying when this happens because the 'Not Referenced' channels are not obvious until
you run into a problem, and then you have to hunt them down. This can be time-consuming with a complex rig or scene.
It's bad enough when this happens to a single user with a small project, but it can be very disruptive to a team of animators on a bigger production because a TD will then needs to go around and check everybody's scenes.
Fortunately, it doesn't happen often, but I see it often enough that I consider it a serious bug. I really
hope they can get this one fixed ASAP.