Hi Shawn,
I tested this out and the calculations are consistent with QuickBooks. I believe what you might be seeing is the difference between how Markup and Markup% are calculated. While Method has an amount field, this is actually the total for the estimate line. The amount field you see in the screen below is the actual amount field, which is cost x quantity. The total field below is the amount + markup.
For instance, if the markup like above is 20% and the amount is $80, $16 dollars is added to the amount to make $96. If the markup is $20 dollars, the total is then $100.
I hope this help clear things up.
- Adam