Failure to pay Estimated tax penalty is overstated by TT

I received a notice from the IRS that stated we had overpaid our "failure to pay proper estimated tax penalty" .

We received a refund.  TT calculated it at almost three times the actual amount.  

This has happened two or three times in the past few years and the IRS has always caught it. I've looked at the "annualized" method and it doesn't apply to us. 

What could be going on? 

Thanks!