@llstalker - Was anything in box 4 on your 1099-R? If there was then that is NOT estimated tax and you do not enter it anywhere else except on the 1099-R box 4. That will carry to line 64 on the 1040 form. Estimated tax paid goes on line 65.
TurboTax did not double count anything, it counted the tax withheld and the additional tax that you said you paid for estimated tax - two totally different taxes.
Tax *withholding* and *estimated* tax are different and separate and have no relationship to each other. You only pay estimated tax if there was no tax withheld. Having tax withheld eliminates the need to pay estimated tax. Just like W-2 withholding.
If you actually sent estimated tax payments to the IRS then it should be on line 65 on the 1040 form and would increase your refund or pay any tax owed. If you did NOT pay the estimated tax then you need to file an amended return and will probably owe additional tax.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**
