IRS charged me 1120S/1065 late penalty even I filed extension

Dear experts,

      I filed two extension forms 7004 to request automatic extension for my 1120S and 1065 filings (two separate small business) in January. However, I haven't heard any response from them. I filed my 1120S and 1065 in early September  (before the extension due date). However, I got IRS letters a few days ago that they charged me late penalties for  both businesses! This sounds insane!

    I did not mail the two 7004 forms using registered mail/certified mail, instead I mailed them using regular mails, but I kept a post office receipt. My wife tried to call IRS but the receptionist appeared rude and refused her explanation. She said even you file extensions, IRS would need to approve them.

    What are my best approach to handle this?

 

Thank you for your advice!

 

jxu98