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There are some reasons why both tax returns appear different:    The IRS often fixes errors or updates information, which can change the final amount. Debt adjustments. The amount that lands in your bank account will be less than what’s on your tax forms if you used your federal refund to pay your services fees.  You may want to keep monitoring your refund directly in the IRS website. Here you will see the updated, official amount: Where's my Refund  

IL uses the AGI as an identifier. The state is matching zero to its records and not able to verify you. Next year, you will be able to file with your AGI. Other identifiers IL uses are IL drivers license and IL PIN.  It is a vicious circle needing one of the 3 to file.   You must paper file your first return with IL to establish yourself. Once you have done that, you can get an IP PIN or use your AGI from this year. Be sure to mail with tracking and no signature required.   If you are not filing again next year but may someday, you might want to get the IL Pin to prevent this in the future. Reference: What is an IL-PIN? Do I need it to file or pay individual income tax?

The Thrift Savings Plan (TSP) is employer-sponsored plan (like a 401k), the "aggregation" rules are slightly different than they are for IRAs.   Be sure to enter both 1099-Rs exactly as they appear. Do not combine them into one entry.   Form #1: When the program asks "How much of this distribution was an RMD?", Select "The entire distribution was an RMD."   For Form #2: Select "The entire distribution was an RMD."   By selecting "The entire distribution was an RMD" for both forms, you are telling the program that "This specific payment was required, and the next payment was also required."  Added together, the program concludes that the total satisfies the IRSl.   Check you 1099-R Entries: Open or continue your return. Click on Tax Tools, then Click on Tools (bottom left corner), and finally, Click on Preview My 1040. Check your Tax Summary, and look for Form 5329. If you don't see Form 5329 (or if Part IX of that form is blank), you have successfully bypassed the penalty and reported the RMD correctly.

Thanks. The state is North Carolina. I get a nearly fixed salary every month and tax is withheld from it every month, so I am not sure where the underpayment comes from. How can I see the calculation in Turbo tax (is there a form/calculation sheet) and how can i amend/remove it if it does not make sense?  

You reported the QCD when you entered the 1099-R from the custodian of your IRA, right? You don't report the QCD in the Donations section like winds up on Schedule A.   Is this how you entered your QCD - yes on the 1099-R and no on Schedule A?   Note: on the 1099-R, you first enter the 1099-R, then on the "Do any of these situations apply to you?", be sure to check the box for "I transferred all or part of this money directly to charity". (Note: you must be at least 70 1/2 to see this option). On the next screen, you will be asked how much of the 1099-R distribution was transferred trustee to trustee to the charity.   If so, then please tell me (if you can), on what line on Schedule A this QCD amount appear (lines 11-14)? Also, if you can see the Charitable Org worksheet for this charity, are there any numbers on it?

Following up -- In case there is any confusion, Recharacterization of contributions is not the same as a Conversion, Rollover, or Back-door Roth.  Recharacterization of Traditional IRA contributions that were not deductible anyway because of income limit, and were not previously deducted, does not change the tax liability at all.  Speaking with a Tax Expert on the phone or in chat is not helpful with a genuine software bug, and so I am posting here, and hoping TurboTax employees take note and get this to the developers with the diagnostic token I provided -- which I would greatly appreciate. I'm going to give this two weeks to be fixed, and if it isn't, I plan to prepare the 1040-X by hand myself without TurboTax.  I will then claim a refund under the Maximum Tax Savings Guarantee which includes a "100% accurate calculations" guarantee.

Name the state, so further help can be provided specific to that state  The default for most states is that 1/4 of the required tax payments for the year must be made each period. Withholding is assumed to occur evenly throughout the year. Estimates only count in the period when made.  Thus, with uneven payments, the annualized income installment method must be used if the state allows that method or whatever alternative they offer.   hence, it's possible to owe a penalty even when getting a refund.   

It’s probably too late now but here is how it’s suppose to work for the Online version.   In case anyone else finds this thread.   Or it may help you figure it out.  What did you get charged for?   Was it for a state return? How to use the Online License Code.  It is for federal only. State is additional. https://ttlc.intuit.com/turbotax-support/en-us/help-article/register-activate-services/como-empiezo-...  

Per @dmertz, the self-employment health insurance deduction should not affect your IRA contribution, as it does not affect earned income. However, if you want to try it you would follow these instructions:   Since you entered a Form 1095-A, TurboTax will ask you if the insurance is associated with self-employment income. If you did not pay the insurance premiums from your self-employment income, you can answer "no" to that question and then your insurance premiums will not be deducted for the self-employed health insurance deduction. However, that may affect your insurance premium tax credit if you have one. You will see a screen that says Self Employed with Marketplace Plan? in the Medical section and then Affordable Care Act (1095-A). The question is are you self-employed and purchased a Marketplace plan. Answer "no" to that question.  

@1095shared , absent a letter from the IRS, the general rule is NOT to amend a return till the processing of the originally filed return has been fully processed.  Thus if you "accepted" original return is still being processed and refund no issued, please  wait till that step is completed.   Is there more  one of us can do for you ?