Assessed Underpayment Penalty

[Jacks5]

My return was accepted and I am due a refund, however, after I submitted I noticed that I was assessed an federal underpayment penalty from paying my estimated taxes.  I incurred a large amount of capital gains in Q4 which was paid by the Q4 deadline of Jan 15, but the software did not take that into account and only warned me that I was assessed an underpayment penalty on my state (not federal taxes).  I am using the desktop software (mac, premier) and tried to fill out an amended return, however, when I update the Underpayment penalties section it (correctly) shows that I no longer owe the penalty but says that form 2210 must be submitted with my full return and the federal refund balance for the amended return remains at $0.  Is there a way for me to recoop the underpayment penalty I was assessed?  Also, I find it frustrating that the software warned that I was being assessed an underpayment penalty on my state taxes, but no such warning triggered for the federal portion.  The inconsistencies give a false sense of security that the software is accounting for possible user oversight.  

[Mike9241]

the software uses the default method which means 1/4 of your taxes is due each period. to avoid or reduce the penalty you must use the annualized income installment method on page 3 of the 2210, you'll need to check box C on the 2210 to use it.  Then when your return is fully processed file an amended return. 

[VolvoGirl]

I don't think you can amend for that.  It is just an estimated amount.  The IRS may refigure the amount and send you a refund (or a bill for more).  They sent me a refund once.