What you are looking at has nothing to do with 1099. What you describe is:
When we entered a Name, we entered that we already owe them, instead of entering a Bill to pay later. They still show we Owe Them, as an AP balance.
Opening Balances indicate you added a value out of thin air. Apparently, you also never Paid these people for that amount. Example:
You put a Name and also Added an opening balance. Later, you enter the bill. Later, you paid that bill. That means you put the Amount you owed them in twice, using two different methods, one of which is now sitting as negative Equity, because you seem to still owe them in AP.
And of course, having paid any vendor name properly using checking, cash, or paying their bill using banking or cash, means that is available data for the 1099.
Meanwhile, you still have Unpaid AP. It helps to never use the function of Opening Balances. Always make actual entries. Have you run your AP Aging summary or Detail report, lately?
