The code we were using when we came to this conclusion is here:

$('.MyTable').on('change blur', function() {
        var rows = $('.MyTable tr').length;
        var files = (rows / 2) - 1;
        var elements = $('.MyTable .file-del').length;
        console.log('Rows ='+ rows);
        console.log('Files ='+ files);
        console.log('Elements ='+ elements);
        $('#q79 input').val(elements);
        $('#q23 input').prop('required', true);
    });

Now that I fiddle with it some more, it appears that it is more about the timing of the calculations. In preview, I'm seeing the file upload almost instantly. So the calculations happen after the table has added the row for the file. When we run the process, the files actually upload therefore taking longer for the table to update and the calculations are premature and finish without the new file included.