Your "refund meter" may not be updating right away. This could be an Internet connectivity issue. Also, be sure you are looking at the Federal meter.
I just tried this with a test Form 1099-INT. The Federal tax went up by the same amount whether I entered the income in Box 1 or in Box 3.
Since the refund meter may not always be reliable, you can preview your return before filing to find out how your taxes were calculated. See here for details.
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