YTD 2019/20 reporting error with ATO

Not sure on how to explain this but I have 1 employee and he is unable to get his accountant to lodge his Tax for the 19/20 year as his report says' Not Tax Ready'. He called the ATO and they dismissed it as it has something to do with Reckon STP reporting.

There seemed to be a double up of some entries as it looked as though the September 1-19/ 2019( 3 weekly pay runs) pays were duplicated. This figure was already included in the YTD figure and another file with just these 3 weeks were also shown as reported. This has since been rectified from our end and when i check his report on my phone app it all looks fine NOW.

However, The ATO are still seeing 2 seperate entries. See pic below from what my employee is seeing when he logs into his MYGOV.

However, im not sure why the ATO are still seeing the old figures. Ive tried calling Reckon and they have been no help at all.

I have no idea what to do and Im not very good with this accounting issue. Regards Alex

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