IRS changed what appears on Line 4a (if the gross and taxable amount for an IRA dist was the same, it didnt appear on Line 4a, only 4b), but I dont think thats where your issue lies.... what showed on Line 4b?  Thats the taxable amount.

Did you have basis for the IRA (that was previously non deductible) that reduced the taxable portion?

Youre going to have to follow the money, look at your 1099R worksheets and the IRA worksheet and see what happened that didnt put the correct amount on Line 4b.