By the sounds of this, you are more experianced than I am with GCPs anyway, but incase it's useful:
I've seen loosly similar results when I've had a point with a substantial error in it, have you checked all the input data for anomalies? Best place to start looking would be to sort the GCPs by error, and turn them off one or two at a time starting with the worst ones then refresh, and see if everything pops into place.
I've seen it where the turned off point is then reported to have an error of nearly exactly a meter, and it turns out to be a simple typo. (university, student projects, we usually end up with the points written down with a pencil in a notebook as it's less of a learning curve)