This question and responses was very helpful.  I too had vendors showing up on the report but then not having 1099s created for them.  Very frustrating as I had already troubleshot all the aspects listed here.  But the comment about subcategories led to the fact that I had designated a specific category in the details of the two missing vendors.  Once I removed that from the vendor description details for each of them (even though the account I had put for each of them was in my list of NEC accounts to map and was not a subcategory), Intuit 1099 found both of them, added them to my bill and created the complete list of forms for me to file.  With this discussion thread I didn't have to wait until Monday to be able to call Customer Support. Good luck to all who are struggling with this!