Pay runs and STP reporting to the ATO are different on the MYOB system.
Pay runs are normal calculations, but
STP reporting is treated as zero.
So when I went to report BAS to ATO,
I found that the BAS reports in MYOB and the STP reporting to the ATO were different.
The BAP reports generated by MYOB were based on pay runs.
However, ATO was pre-filled based on STP reporting, so the PAYG was calculated as almost zero.