Same thing happening here. I tried deleting "three lines down" and that did not remove the duplicate amount. I ended up leaving the check amount blank in the top section (on the virtual check) and just putting the amounts in the line items below. That auto-filled the virtual check to the correct amount.
Granted I only needed one line item. I hope it works when I have multiple line items for a check.
If all else failed, I suppose I would have gone in and created a "bill" and then paid it that way.
