STP YTD report & Payroll Summary report discrepancy

Prior to STP reporting being set up, 3 employees were terminated. 

Their final pay included unused leave entitlements and an ETP component with ETP Tax Withheld. At the time of processing, the option to select ETP type O didn't appear despite the STP categories being linked to each pay item (ILON, Unused RDO).

Once STP reporting was set up and an Update Event was lodged, we found that only the unused annual leave portion of the final pay appears on the employees' Summary of Payments but not the ETP info. The Payroll Summary Report confirms the amounts were processed against the correct STP category.

For STP finalisation, the Payroll summary report doesn't reconcile to the STP YTD verification report. The ETP components aren't included. Following the instructions for Fixing an ETP doesn't help as we can't reverse pay (option not avail/greyed out).

During a call with MYOB support this morning I was told to record a duplicate pay for each individual with just the ETP values, using the exact same dates as originally processed. However, from an accounting perspective, recording a duplicate pay would affect all pay reports' YTD figures, would it not? The Payroll Summary, Pay Activity and Payroll Register would then be over by those same amounts.

There has to be a more logical solution. Appreciate any help to resolve this asap as I've been waiting since 10th July with an open support Case but no call back.