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Since 1040 and 1040-X are processed separately you should expect the refund shown on Form 1040. That's why it is appearing on your 1040-X which will take several months to process.   I assume you meant to say "not allowing" rather than "now allowing"   @shop3   

You might be able to eliminate it or at least reduce it.  You can go to Federal Taxes tab or Personal tab, under Other Tax Situations and select Start by the Underpayment Penalties. You will answer a series of questions that may reduce or eliminate the penalty. Or you can elect to have the IRS figure the penalty for you.  It's form 2210.   It's under Federal or Personal (for Home & Business Desktop) Other Tax Situations Additional Tax Payments Underpayment Penalties - Click the Start or update button   If you have the desktop program you can switch to Forms Mode (click forms in the upper right (left for Mac)) and open the 2210 form.  If the 2210 doesn't show up in the left column, click on Open Forms at the top of the left column.  Type 2210 in the search box and open the 2210 form.  Check box C if you want to let the IRS calculate it.

did you enter the April payment under Deductions & Credits / Other Income Taxes / Payment with 2024 Federal Extension   April/extension aside did you have a penalty due to underpayment in 2024, if you didn't withhold enough or pay timely (quarterly) estimated taxes to meet the safe harbor amount (smaller of, 100% of your 2023 tax [110% if AGI > 150k], or 90% of your 2024 tax)?  Paying it all by April does not avoid a penalty if you didn't pay enough thru the year - underpayment penalty is calculated on a quarterly basis thru the year.   If your income was uneven during 2024 and you had some sort of large income event late in the year such as Roth conversion or cap gains, you may be able to reduce the penalty by adopting the "Annualized Income" method on Form 2210, tho if you simply underpaid in 2024 it will not entirely eliminate it.   If you can provide more information on your situation based on the above then it will be easier to provide more guidance if needed.

if your extension request susbmission was successful, your  Account Transcript statement on your own account at IRS will show that. If you don't have an Online account, you can ask the IRS to mail the  Account Transcript to you.   @GGGGary554 

You cannot download an old W-2 from TurboTax.    TT does not have copies or images of your W-2's.   Only the data that was entered when you prepared the tax return is on the worksheets;  TurboTax does not ever have copies of your W-2's   If you need a copy for some reason, ask the employer, or seek one from the IRS for a fee of $30.     I NEED A COPY OF MY W-2  (or 1099)      W-2's come from employers.  There is not a federal or national website that provides W-2’s.     TurboTax does not have a copy of your W-2—the Wage & Tax Statement—issued to you by your employer, (nor does TurboTax have copies of your 1099’s).   You should always save those documents for your own records. You could ask the employer(s) for copies or you can get a copy from Social Security (for a fee of $62).   To get a copy of a W-2 from Social Security https://faq.ssa.gov/en-us/Topic/article/KA-02501   https://www.irs.gov/help-resources/tools-faqs/faqs-for-individuals/frequently-asked-tax-questions-answers/irs-procedures/transcript-or-copy-of-form-w-2/transcript-or-copy-of-form-w-2     If you saved a pdf of your completed tax return, the worksheets will show the W-2 information you entered, but not the actual W-2.   You can get a wage and income transcript from the IRS:  It will not show the actual W-2, 1099’s, etc, but will show the income information the IRS received.  It will not, however, show your state information. It will only show the federal information. https://www.irs.gov/individuals/get-transcript   Or you can pay the IRS $30 for an actual copy of your tax return which will include copies of your W-2’s      https://www.irs.gov/pub/irs-pdf/f4506.pdf      https://ttlc.intuit.com/turbotax-support/en-us/help-article/tax-forms/get-copy-w-2/L8FTim9MO_US_en_US?uid=m68ee4os  

If "services" are provided to the tenants (such as maid service or meals), it is entered as a business on Schedule C.   If "services" are NOT provided to the tenants and you do NOT "Materially Participate" (somewhat uncommon), you enter it in the rental section.  Use 39 year (commercial property) for the depreciation.   If "services" are NOT provided to the tenants and you DO "Materially Participate" (most common scenario), TurboTax is not set up correctly to report it.  You may want to try a tax professional or some other software.

@billnorthraleigh wrote: or comparable to those given by IRS and Quicken Tax Planner.   Out of curiosity, why don't you just use the other planners that are more trustworthy?   https://www.irs.gov/individuals/tax-withholding-estimator