Did you pay the amount that was due on the original return? Amended returns assume that tax has already been paid (or any refund has already been received) and the amended return only shows the difference between the original and what you corrected.
Look at Line 16 of the 1040X, that's the line that shows what was paid with the original return. If that line has a dollar amount but you didn't pay that, then the IRS is correct and you still have a balance due.
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