A likely cause is that the camera is in a mode where AF point selection behaves differently.

On the 5D Mark II, AF point selection should normally work in the creative modes: P, Tv, Av, or M. If the camera is in full auto or another automatic mode, some controls may be limited.

In your case, the camera was apparently set so AF point selection was being controlled with the rear multi-controller (the small joystick/nub near the back screen) instead of showing the change on the top LCD in the way you expected. The selected point could still be changed, but you would mainly see it through the viewfinder.

So check:

• Exposure mode: use P, Tv, Av, or M
• Custom/control settings affecting AF point selection input
• The viewfinder, since the active point may still be changing even if the top LCD does not show it as expected

If needed, compare the custom function/button settings with a known-working 5D Mark II or reset custom settings and test again.