I'm posting this incase it affects others.
I noticed a discrepancy between my July bill and the amount automagically paid for that bill mid August.
As a hypothetical example, my bill was $550 for the month, however the amount I paid was only $500 when the 16th of the month came by because there were some credits applied in the meantime.
This causes a timing issue because I have a "receipt" for the $550 and relevant HST paid, but the transaction for the payment is only $500. So accounting wise I have to do something to undo the credit amount because my bill and bank balance are out of synch.
I did try to download a copy of my transactions to figure out what was in the credit (I have too much stuff to look at it directly), did that a couple days ago and am still waiting to hear that it is ready. Downloads seem to take a very long time to be ready!
Anyway, in the meantime I did go and find these two options is in the "Seller Billing Preferences section and sub tab":
Please choose your automatic payment amount for the current invoice:
which gives these two options:
Apply recent payments and credits to automatic payment amount
Recent payments and credits will be deducted from the amount due before processing the automatic payment
OR
Apply only recent payments to automatic payment amount
Recent credits will not apply to the current amount due and will be deducted from your next invoice
Mine was set to the first which is what was causing my timing problems.
I've changed it to the second,which I think means the payment will now match the "receipt" I got.
Assuming I have this figured out properly you may wish to do the same to keep you (our your accountant) sane.....