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I have a number of invoices with a 0.01c outstanding balance as there was a difference of that amount between the calculated GST on our manual invoice versus the GST calculated by MYOB when we entered it... is there a way of fixing this?

You can actually manually override the GST amount on an invoice.  Open up the invoice first, then click on the white arrow next to the GST amount at the bottom and change the amount. 

This is very handy in those fiddly situations where there is a rounding issue, but you should never change the GST amount by more than a few cents.

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