Hi trevor-lindley,
The way that the GST centre calculates the GST on your BAS reports is by looking at the tax codes that are assigned to each transaction in your company. This is regardless of the account that the transaction has been allocated to - even if an expense were allocated to a Sales account, for example, as long as the tax code was set to GST on Purchases, the GST centre would include the expense in the GST on Purchases and it would be included in that section of the BAS.
The Profit and Loss report, on the other hand, only looks at the account balances of the relevant accounts for the report. The report is run exclusive of GST, so the GST amounts are not included in any of the figures that are shown on the P&L, and the income amount that is displayed will be shown excluding the amount of GST that had been calculated on those amounts.
Feel free to reply in this thread if you have any more questions about this!
-Lucas
