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Be aware that in some states it can take several weeks to process an amended return, especially if they review it manually.   If due a refund, see if it shows up in Pennsylvania's refund lookup tool.  I don't know if an amended return will show up there or not. https://ttlc.intuit.com/turbotax-support/en-us/help-article/tax-refund/track-pennsylvania-tax-refund/L30ffN4ke_US_en_US   Or phone the PA DOR to inquire about its status and how to check on it in the future.  The phone number for "Personal Income Tax" is shown in the table at: https://www.pa.gov/agencies/revenue/contact-us/contact-us-by-phone.html

Only Kansas DOR will know what all they are doing with your return.   Some states are fairly quick with refunds, while other states can take a long time processing returns--even several weeks--as they crack down on detecting fraudulent returns.     Here are some things you should check before phoning your state's department of revenue:   First, you need to be sure your state return was successfully filed.   If you efiled, be sure your efiled state return was accepted.  If you used Online TurboTax, you can check by looking at the Tax Home in your Online account.   Or did you choose to file by mail instead?  TurboTax does not mail it for you.  If you chose that method, you have to print, sign, date, and mail it.   The FAQ below tells how to check on a state refund and has a link for your state.  Then you'll see information for your state (which may include info on how long it takes in your state) and a link to go to your state's "Where's My Refund" tool.   It may also have a link to your state's department of revenue.   Your state may also have a FAQ section at it's "Where's My Refund" site that tells how long to expect in your state, and how to contact them to inquire.   Choose your state from the table in this FAQ: FAQ:  How do I track my state refund? https://ttlc.intuit.com/turbotax-support/en-us/help-article/tax-refund/track-state-refund/L3jgO8PGs_...

In IRS Direct Pay I flagged it as Estimated Tax. In TTax it is entered under "Tax withholding that you haven't entered yet", Federal withholdings.  I did not enter them under Estimated Taxes because I did not file a form 1040ES.  I can see this may be a possible cause for my problem.   And since I don't have wages I don't have normal withholdings.  My normal withholdings are determined by a % that I elect when setting up my RMD and pension plan payments.  I've never in 20 yrs of retirement filed a 1040ES as I've always made sure I was covered by withholdings of the individual payments.   But my real problem is how to get the IRS to accept that I don't deserve to have a 6 figure refund which is quoted here "We changed your 2024 form 1040-SR to match our record of your estimated tax payments,".  In other words, they see it as an estimated tax payment.   So on my return, I entered the amount on line 25c and apparently I should have entered it on line 26.  Is that a correct assumption?

@PatriciaV Thank you for the further advise. While I try to follow the suggestion using TurboTax (Premier on Win and Business on Win), I encountered the following: 1) " ... Depending on the state, you may need to include the tax payment on the K-1 from the LLC."  I can't figure out how I can include the tax payment info in the K-1 of my LLC generated by TurboTax Business. I went through the interview questions and can't find it. Does it suppose to go to Box 15 (credit)?  2)  "When you complete the state income tax interview for your personal return, look for questions under the K-1 topic that relate to tax paid on your behalf by the LLC." Again in the Individual return (TurboTax Premier), on the "State Tax" tab (NJ), I went through my LLC K-1 part, and did not find the tax payment related interview questions.   So far I can enter the amount of the state tax paid as you initially suggested during in individual Federal Tax ("other tax .... tax paid not reported in W-2/1099 ..."). But as I mentioned, I am wondering if the tax paid via my pass-through LLC can be entered this way.    Thank you for any further suggestions.