payroll tax putting out reconciliation

When I process my payroll, I normally do a spend money (cash) as I process the payroll. All year I have not had a problem with reconciling at the end of the month.

For some reason, this month (June), when I tried to reconcile, I found in the transaction journal, that the pays for the month, were under the payroll tab. (I dont know what I have done for this to happen?). It is title "pay employee" and has the gross amount , tax and super items in there.

But I also had the spend money transactions that I normally do when I process the payroll, so doubling up on the pays.

I can not delete the transactions under the payroll tab, as it says they have been sent for STP.

So I deleted the pays I had done through spend money, thinking that would even it up.

Then when I tried to reconcile, the amount I am out of balance is the exact amount of tax calculated for each pay during the month.

I am not sure what I do to correct this?