On Form 1040, the standard deduction is shown on line 12a; the charitable contribution allowed with the standard deduction is shown on line 12b; the sum of these two amounts is shown on line 12c and subtracted from your Adjusted Gross Income.
The refund meter/balance due amount is constantly changing as information is added to your return. It is likely that the change was just not noticed at the right time with regard to the refund being adjusted for the charitable contribution.
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