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Firstly ensure that the correct system reference is set up to identify whether you are Accrual or Cash Basis GST. GST  
GST Tax Codes are Linked to the Relevant Bas Codes. The
The GST Batch works off all the entries that have flowed through into the GST file. For GST Cash Basis, the GST is taken into account when the GSTCASHBASISDUE date is marked on each Open Item when a Payment has been allocated against any Open Item. For GST Accrual, the GST is taken into account at the time the Open Item Invoices are Finalised. Once
Once a Batch is Extracted and Posted, the Invoices are stamped with a flag so these open items will not be accounted for in the next GST Batch Run. First
First of all Run a GST Detailed Report or go to GST Items and filter correctly before you attempt to Extract a GST BATCH RUN. 

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