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@VolvoGirl 

You say that it's common and normal and expected for the IRS or state to bill you for more or send you a refund.

How does the IRS decide to bill you? vs take it from the refund and send you the reduced amount? 

Isn't it the case when there's a refund  and TT says that it has subtracted the penalty from the refund, and the refund is now that much less, that the TT return, when submitted, a) goes through successfully to the IRS, b) the IRS accepts the return, and c) the IRS deposits the refund minus the penalty in your bank account?  

 

Or does the IRS still refund the full amount and send you a bill for the penalty, even though you did not check the "C" box ("Check to have the IRS figure the penalty and send you a bill if a penalty is due") on Form 2210 : Underpayment of Estimated Tax?