When applying multiple tax rates to an invoice both BPro and QuickBooks will round the result to 2 decimal places, but in some cases may come up with different values. This occurs because QuickBooks will round the result of each tax differently than BPro does and this can result in the QuickBooks Invoice being 1 penny less than BPro.
The invoice itself will sync over to QuickBooks without an error, however, you may receive an error when attempting to sync the payment(s):
To resolve this you will need to modify the QuickBooks invoice so that it will match BPro and then you can sync the payment over by clicking the "RERUN" button on the Transaction Log and running the web connector update.
For more information on how QuickBooks calculates taxes when multiple rates are applied please refer to their support documentation.