it’s slightly difficult to know exactly what you are doing and what is going wrong from your description.
Note that the macro works on the currently selected peaks. So if you pick peaks with PA and then realise that some of them are noise peaks and you delete those, then the other peaks that were just picked are no longer selected (highlighted with a box round them). So you will then have to re-select those peaks (with Ctrl/Cmd + left-drag) to run the carbon assignment macro - otherwise it won’t work.
Hopefully, that solves your issue (though if there are no peaks selected, the macro should tell you so).
I don’t quite understand your comment that
the C shifts never show up in the Chemical Shift table, although the chemical shift table shows that it knows about them (e.g., the “Total Peak Count” column shows 13).
What do you mean with “them” - Carbon NmrAtoms/Chemcial Shifts or peaks? How can you get a Peak Count (indeed a row in the table) without a Chemical Shift? Or is this for the H and N Chemical Shifts that you see the Peak Count?