This is a common annoyance affecting anyone using vendor discounts. It’s an issue in Canada (not the US), and my hope is that it will be fixed in the near future!
When most users enter a BILL, they typically enter the information in order; in other words, the way QuickBooks guides you through entering the bill if you tab from field to field. That means that the AMOUNT of the bill is typically entered on the top portion where it says AMOUNT DUE.
However, if you enter a bill this way AND use vendor discount terms (ie 1% 10 Net 30), the amount of the discount will NOT show up when you go to PAY BILLS. This is a known issue that QuickBooks Canada has yet to fix.
When entering a bill using a vendor discount, DO NOT manually populate the AMOUNT DUE field on the top of the bill. Skip past this field and enter the $$ information on the bottom half of the bill. THEN CLICK RECALCULATE. This method will ensure that your discount will show up in the PAY BILLS window.
Do not manually populate the AMOUNT DUE field if you want your vendor discount to show up in the PAY BILLS window.