Shapes' positions are calculated relative to the zero point of the rulers. That's controlled through the box in the upper left of the drawing where the rulers meet. (Rulers have to be visible, of course: View>Rulers or command-R.) Drag out of the box to move the zero point. The new axes will show up as blue lines; their intersection is draggable for further changes. Double-click on the control box to reset them.
See this thread for discussion of stroke vs. shape boundary:
http://forums.omnigroup.com/showthread.php?t=18719
The stroke is centered on the shape boundary. The control handles remain on the boundary, so you can see the relationship by zooming in far enough.