STP finalisation error

HI DebPW 

Thank you for your post. And welcome to the Community Forum. 

I understand that your Payroll activity report and Payroll Register report match but the YTD verification report shows a different amount. To provide you with some information, the payroll activity report gets its data from pay runs through Process Payroll. The Payroll Register report gets its data from the Pay History tab on the employee card. The YTD verification report gets its figures from the Pay History tab. (same as register) and filters those figures using the ATO reporting categories. 
 

When the Activity and Register report match but the YTD verification is different, this indicates the figures are correct in the software but are not being filtered correctly by the YTD verification. You will need to run the Activity Detail report to narrow down which category is causing the issue and then check the ATO reporting category is correct and hasn't been exempted from PAYG. 
 

Another step is to try processing $ pay to update the YTD amounts in STP. If you have sent old reports, this will send the YTD amounts from that period, overriding the YTD amounts in the last current report you sent. The ATO uses the time stamp of when a report is sent to determine which is the most recent report, not the pay period in the report. If you send a June report today, the time stamp will be today and the ATO will take that as the current report but the YTD amounts are from June.
 

About the ATO business portal. The important thing to check is that your YTD verification report reconciles with your MYOB payroll reports before finalizing the EOFY. It's the YTD verification report that is sent to the ATO. You can also confirm that the ATO has the correct YTD amounts by getting your employees to check their myGov accounts. 

You can also check this Article:  AccountRight reports don't match my STP reports

I hope this helps. If you need further assistance or if the information I provided did not fit your issue, feel free to post again so I can investigate the issue. 
 

Thanks,

Cel