Filing forms 941 and 940?

I have been calculating FUTA and paying through EFTPS. Business started October 2011. I recieved a notice from the IRS saying I had not filed a form 940 for 2011 although I made payment for form 940 (have the confirmation) back in January. Do I need to file paper forms for these along with making an EFTPS... show more I have been calculating FUTA and paying through EFTPS. Business started October 2011. I recieved a notice from the IRS saying I had not filed a form 940 for 2011 although I made payment for form 940 (have the confirmation) back in January. Do I need to file paper forms for these along with making an EFTPS payment? Is there any way to file the 940 electronically for free (no additional software or subscriptions)? Am I going to get letters from the IRS saying that I have not filed 941 forms if all I have been doing is paying those through EFTPS?

Since the IRS seems to want to move businesses and individuals to electronic filing, I'm surprised this seems harder than it needs to be if more than EFTPS is involved.
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