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I explained the possible lost 1000 somehow on the 1040 and mailed a copy to them as they requested, their response was:  "Before we can resolve this matter, we need to process all of your information.  We'll send you our complete response within 90 days.  We don't need any further information from you right now."  This is 2 - 90 + days now and they are charging me interest.  I'm not understanding your tax vocabulary, but it's rather obvious to me that they don't have this particular 1099.  If I send the 1002 in plus interest will I ever get it returned if I am right