Billings (and indirectly commissions) are calculated based on the total invoiced amount and not the vacancy Fee or timesheet Client Services. If you have issued a credit note or additional invoices and have not adjusted consultant commission and contractor payments then you will get incorrect results. The easiest way to find these anomalies is to run the PRS Audit Report (in particular see audits 103, 105, 107 and 108).
See also the Billings and Commission Calculations sections of the PRS Essential Reference.