The P&L report looks at transactions posted to the income and cost of goods accounts, while the GST report runs the sales figures based on the tax code used in a transaction. If there are transactions coded to other type of accounts while using GST tax code, or transactions with the correct income/cost of sales account entered but wrong tax code used, they can cause difference between these 2 reports.
Additionally, both can be run on Cash basis or Accrual basis, please make sure both reports are using the same accounting basis before comparing.
I'd suggest running both reports on smaller periods, e.g. month by month until you can locate the period the difference ocurred, then look further into the transactions recorded in that period.
