It sounds like you're using the View Options tab in the gradebook settings menu to sort your columns the same way that assignments are sorted in the Syllabus course summary. In the Syllabus tool's course summary, all assignments without due dates show at the bottom of the list in alphabetical order. Is it possible that some of your assignments have no due date set? If so, they will show to the right of (i.e. after) the columns with due dates, and they will be sorted alphabetically.
Another view to try is opening the Assignments index in Student View. The default student view of the Assignments index separates dated and undated assignments. This may also be helpful.