I am having the exact same problem. A vendor is showing up (correctly, with the correct over-threshhold amount) when I "Prepare 1099", but, that same vendor and the related transaction is not in the "1099 Transaction Detail Report". I've adjusted settings for the report. Difficult to reconcile the 1099 report to the actual 1099's prepared. Kind of assumed the numbers would be the same, or differences would be easily identifiable. 

Any idea why QBO would prepare a 1099 for a vendor but not have any transactions in the 1099 Transaction Detail Report?

I've read all of the comments, so it's not necessary to re-post the standard instructions.