If we have some vendors set-up for 1099 purposes, but used various categories for payments to them. Why didn't the 1099 program reflect all payments to these individuals?

1. each vendor must have 1099 tracking turned on

2. during the 1099 creation wizard you are asked to track expenditures to various blocks on 1099 (or map all to Box 7)

3. credit card and merchant processing payments (like PayPal) of vendor bills are excluded from 1099

4.  only payments totalling $600 or more will generate a 1099

@mts2 Great question and kudos to @john-pero for the response!  The information provided is correct, if you would like additional information on proper setup for contractors here's an article that can help you with vendor setup and 1099 preparation. 

Find your vendors when you prepare your 1099s