2020 Tax refund not applied to 2021 taxes owed?

I had tax refund  of lets say $1000 for year 2020 taxes and I applied that refund towards 2021 taxes. It went fine. But I ended up filing for extension and I got additional $100 refund and I also applied that refund towards 2021 taxes.

 

I filed for extension for 2021 taxes and have not filed my taxes yet. I recently got $100 + some change (interest rate I assume) check from IRS and I was bit surprised to see that check. It took almost one year for check to arrive and I forgot what it was about. I did some searching and finally figure it out it was refund which came from extension filing portion.

 

I did check Turbo Tax (download version) and in the software (under Other Tax situation and Apply refund to next year) it was cleared listed $1100 ($1000 original and $100 extension refund)  refund  will go towards 2021 taxes but it did not. Then I checked all forms  in forms mode and there in form 1040 X- line 22 it was marked $100 will be refunded to me.

 

But in same extension filing after 1040-X there is regular form 1040 also appear with all new figures. In that form line 34 under refund section clearly list $1100 ($1000 with original and $100 extension)  will be applied towards 2021 taxes and 35a amount refund as $0.

 

Q. Is how this happened? Software is showing something else and under IRS forms 1040X and 1040 has conflicting information.

 

Q. Should I deposit this check or send the check back to IRS stating to be applied towards 2021 taxes. I assume this will make it more unnecessarily complicated?

 

Q. Now I am preparing for 2021 taxes. TT imported data form last year. TT imported $1100  refund applied towards 2021 tax year in payment section. How can I correct this amount to $1000? I guess software is not computing numbers correctly, do I have to check and change via forms mode on my own?

 

Q. Since IRS sent me refund and some change in interest payment. Will I get some sort of from from IRS for interest rate portion and when will I get one and for which tax year?