problem with efiled return not matching printed return

[user17570262219]

I am a notary.  On schedule SE, line 3, the programs prints a notation: "Exempt- Notary" and the amount of income from Notary services.  It has been this way in previous years, and the copy generated from the program for my records shows this. However I received a notice from the IRS and after many calls was told that the copy they received (efile) does not show this notation.  Is there an issue with the efiling that this would happen?  I mailed them a copy of that form from my records, but of course have not heard back.  

Again, I want to know how this could happen.