Hi penejane
Thanks for your post.
Kindly check the Payroll Activity Summary report if it matches your Payroll Register Summary report. Once checked, please have a check as well of the ATO Reporting Category used for the Payroll Categories. If the allowance were recorded as Non Reportable, then it will not show to your YTD Verification Report. In EOFY Finalisation tab, against each employee you will see three dots which you can click. It will allow you to view the Individual Summary report. This is the the breakdown of other pay items that is not reported as Gross Payments.
Please let me know if you need further assistance.
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Best regards,
Doreen