For anyone else having this issue, check the TAX PAID WITH ORIGINAL RETURN field on the 1040X form. The program was populating that field with the tax owed amount, even though that was not correct. I was able to delete the amount paid and enter the correct amount.
However, there's still something else going on... it's populating Column A (Original return info) with numbers that did not match my original; there are numbers populating the changes Column B with numbers that I did not enter and can't tie to. I'll have to keep researching this.
