Huh ???

What $ 40,000 threshold are you talking about?  

Are you talking about the first tier of capital gains is taxed at zero?   If so, that doesn't mean the 'rest' of the gain isn't taxable.

Or, if I'm wrong ... I have a LOT of amended returns to do .

Take a look at the Sch D Tax Worksheet to follow the math.  I assume ProSeries follows the one at the end of the Sch D instructions.  You'll see on line 22 "This amount is taxed at 0%."  Keep following and you'll see the other rates as well.

Same client?

https://proconnect.intuit.com/community/proseries-tax-discussions/discussion/home-sale-worksheet/00/...

That 231k gets added to the income for cap gain 0% tax income limit....shes NOT below 40k.