We have just noticed that when we go into a payment to edit it (i.e. we add a comment onto the payment) it marks it as 'published' when we hit 'Save and Close'.
As all of our payments are taken offline we need this to work correctly as
1. it is how we monitor which payments are outstanding
2. It sends a reciept to the buyer when marked as paid, which we obviously do not want it to do untiil we manually publish it.
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