Back in early 2000's, I mailed a paper return in. Months later received a notice that I owed a penalty of underpayment of estimated taxes. Protested that they were incorrect as I had uneven income that year and according to Schedule 2210AL, did not owe any such penalty. Come to find out that they had no record of the 2210AL being filed......in the transcription of the paper info into the computer system, they "lost" it. First thing IRS does (after removing any checks/money) is to enter your tax info into the computer system. After that six months of back and forth hassle, I became a strong proponent of electronic filing. And with IRS budget cuts, I expect any manual processing to get worse.