I had the same issue and after various attempts I finally found one that worked. In my case I had an invoice entered with a $140 line item and another line item for a $3 credit (actually I'm using the CDN version so the credit was HST ITC which might have contributed to the issue being a -ve amount?). When I deleted the difficult invoice and set it up instead as a new invoice and new credit, I was able to clear the paid bills item. Just be careful to first void the payment before voiding the problem invoice. All good now!
