Check the master page. Perhaps there are two of the items there. Perhaps the master page is based on another master and the item is on both masters.
No, there's not an extra copy on the master.
The thing about this, is that it'll make infinate copies of the master item. Every time you command-shift-click on it, you get another (editable) copy, but the original always remains.
SOP for a file misbehaving is a pants down spanking*.
*PDS = export to .idml and re-open that file and save.
I'm not quite sure I follow the SOP part, but exporting it as an .idml file did the trick.
I guess it was a bug and not a feature!
thanks for your help,