Do you have the interest and penalty calculated as part of the return? If yes, the balance due in the letter should include them.

The program is calculating the penalties and interest but only showing the tax in the letter.  however, i am doing a 1040X and i wonder if that makes a difference. It shouldn't since the summaries both show the penalty and interest calculations. 

It just creates additional conversation with clients when the letter does not equal the tax return or the summaries, and they have to call to find out what amount to pay.