Ok, listen. When you duplicate them, they will all have the same center, the center they were duplicated from…if I remember correctly.
So before you do the new center button, you must make them all their own object.
In object mode, object menu/clear-apply/make duplicates real.
Then do the centers.
I never had one of the little guys jump up on another one. How did you make that happen so I can duplicate that and help?
When you first make an armature, with the add amature, it will be placed where your cursor is positioned.
To move its center, in object mode, position your cursor where you want the new center to be. Then with the armature selected, go into the object menu/transform/center cursor.
Your cursor is lost? Pick anyplace on the screen and RMB and it should be there.
To place your cursor in the center of an object, select the object and then go to object/snap/cursor to selection.
To find a center between objects, select the objects and do the same. The cursor will snap to the middle point of your selection.
Hope that helps.