Retirement tax questions

I took a look at your sanitized tax file specifically IN form IT-2210A.  I did the calculations by hand and they appear to be correct showing no penalty due.  Below is a screen shot showing lines 13-25, all columns.  Bottom line is with the withholding shown from W2s and the tax payments you entered with dates, the minimums were paid each quarter so there would not be any penalties.  

Be sure you have the most up-to-date version of your TurboTax software.  Click the "Online" tab at top of your page and "check for updates."  Compare the screenshot below with a printout of your submitted return or any calculations from the IN letter you got to see any potential differences.