The IRS gets a copy of the 1099-R they know before you even file what belongs on line 4 ... so the only time you get an IRS letter is when the expected amount doesn't show up ( and in the prior years ... since the IRA was on a separate line from the retirements ... showed on the wrong line).
If line 2 a of the 1099-R is blank or says UNKNOWN then the IRS expects the taxable amount to be the same as box 1 UNLESS you have a good reason for it to not be the same and that reason is on form 5329 or 8606.
In the 12 years I have used the DRAKE professional program, and in the 27 years in the tax prep business, none of my clients got letters from the IRS on this matter since the info was correctly entered and matched what the IRS was expecting.
