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I have a similar problem with TT (H&B Download) not recognizing my payment with my Maryland extension.  TT recognized my federal extension payment as well as my (non-res) Georgia extension payment.  I have entered the correct information into TT Deductions & Credits/other tax situations/state extensions.  In Forms view, it will show correctly.  However, whenever I then try to Save for my records, or Print my return, TT will change the amount paid with the extension to the (lesser) amount due and not show the refund of the amount overpaid.  How do I get it to save and print correctly?