If the Xero invoices do not match the FlexiTime totals, the most likely reason is you have reversed a pay in FlexiTime. When a pay is finalised draft accounts payable invoices are sent to Xero. If a pay is reversed, these Xero invoices are not updated.
You will need to reconcile the IRD invoices in Xero for with the pays in FlexiTime to identify the reversed pay.
To help reconcile the invoices, run the Pay Summary report in FlexiTime (Payroll > Reports > Pay Reports) for each pay in the tax period that's different. The Payment Summary section will show you what the Inland Revenue amount was so you can then change the Xero invoices to match.