Why am I seeing an underpayment penalty for estimated taxes when adequate taxes were withheld from my RMD? Can this be manually fixed? Thank you.

[VolvoGirl]

Is it the excess accumulation penalty for not taking enough RMD from all of your accounts?  That is currently a problem they are working to fix.

Or the underpayment penalty on 1040 line 38?

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

[VolvoGirl]

About your RMD and 1099R 

You didn't actually pay the tax.  You had taxes withheld like from your paycheck. You still have to enter the 1099R and whole gross original amount (before taxes were withheld) with your other income to figure out the total tax (and it may put you into a higher tax bracket) and then the withholding is subtracted from the total tax to figure your refund or tax due.  The gross amount shows up,on 1040 line 4a or 5a and the taxable amount on 4b/5b. The withholding will show up on 1040 line 25b.