Biweekly payroll and quarters

I pay biweekly a week after the 2nd week ends.  So weeks Sept 3-7 and Sept 10-14 were paid on Sept 21.  And now weeks Sept 17-21 and Sept 24-28 will pay Oct 5.  How is Q3 managed in this situation?  I did everything like Sept 21 check was the last payroll in Q3 and closed Q3.  And the Oct 5 check I have started entering, a warning that "The Pay Period Begin and Pay Period End date are in the previous quarter." with option to continue.  Is this normal? I did a test post of the first week, and everything seemed normal.