OK so the problem is an AC programmer gave us a great feature but forgot to fix it to work properly (my opinion).

Check the "Active Only" box, edit the diagnosis with the "Problems Pencil" so that you resolve or inactivate diagnosis.
Close the chart and reopen and here is the problem, all of the diagnosis are back! WHY??????
Why is because it is programmed to open the chart without the "Active Only" box checked.
So go over,check the Active Only box, and voila you have only the diagnosis codes you left after using the Problem Pencil box.