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I had no problem entering the extension payment in the Federal section (desktop Windows software), and the software had it applied to NC.

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A couple thoughts though.   

1)  A software update was issued this week.  Don't know if that has an effect, but make sure you update (mine is updated and worked just fine)

 

2) If you used TTX software in this exact same tax file, to submit your NC extension, and payment, it might already be accounted for.   Switch to "Forms Mode".  Look for and open the Federal "Tax Payments" worksheet.  Check on line 22  9 to see if your NC extension payment is there.  IF not, go ahead and enter it on that line of the worksheet AND, make sure you have selected NC as the state.

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3) if you have filed and paid extension $$ for more than one state...come back and let us know, because special steps are required that differ from #2 above

____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*