Both boxes now rotate together because they share the same modifiers. Look at Figure 1.19. Figure 1.19 Two instanced boxes with XForm modifiers added to the stack. Rotating the XForm gizmo of either one rotates both boxes. Instanced objects share all elements of the modifier stack.
Referenced objects are instances with respect to only part of their stacks.
Turn your instances into references by clicking on the Edit Stack button in the Modify panel. In the Edit Modifier Stack dialog box that appears, click on the Reference Object button. A new line appears at the top of the stack. Click on OK to confirm the change. Take a look at Figure 1.20.