I am also experiencing this issue and would like to be updated on an answer from Xero for when it will be fixed. Currently, I am correcting the Activity Statement (not using the pre-filled ATO amounts) but it is not good that the Xero STP reconciliation does not match the ATO!
I am also experiencing this issue and would like to be updated on an answer from Xero for when it will be fixed. Currently, I am correcting the Activity Statement (not using the pre-filled ATO amounts) but it is not good that the Xero STP reconciliation does not match the ATO!