Hello and thank you for using Just Answer,What paper work does he have that stated the waiver of the penalty due to an IRS problem?
For farmers, if you filed your 2012 Form 1040 by March 1, 2013, and pay all the tax you owe at that time, you do not need to make an estimated tax payment. He would need the documentation that allowed for waiver.If at least two-thirds of your gross income for 2012 or 2013 is from farming or fishing, you have only one payment due date for your 2012 estimated tax, January 15, 2013.If he made that payment then he would have no penalty.
Here is the notice he will need to claim the waiver or abatement from penaltyhttp://www.irs.gov/pub/irs-drop/n-13-05.pdf
The above has the info you will need to assist your brother.