I know this is old but just my two cents. My understanding of the rules on the underpayment penalty is that you weren't able to avoid the penalty entirely. You would have been charged a penalty on the underpayment for Q1 even if you paid it on July 15, but doing so would have minimized it. I believe you would have avoided the penalty had you increased your withholding to equal within $1000 of your tax liability(or the lower of 90% of this year's liability or 100% of last year's). This is because I believe withholding is considered paid evenly each quarter.
This is my interpretation of how it works.
