It's been over a year and Intuit has not resolved this common theme.  The only work around I found for filing 1099s for multiple vendors with 1 EIN is to use a journal entry.  I have 3 vendors set up, only 1 is flowing over to the 1099 report.  I have unchecked the box for the 2 other vendors for the 1099 tracking.  I made the journal entry amount for the annual payments made to those 2 vendors (DR GL account include vendor name; CR same GL account no vendor name).  In the name field the vendor name for which you will file a 1099, the second line does not need to have a vendor name.  I used the same GL account for the entry so it is a zero net impact to reporting.  Run the 1099 report and the correct total will appear and 1099s can now be filed correctly.  Let me know if anyone else has another alternative.  Hope this helps!