Lot Numbers In Stock Report doesn't match Inventory Stock Status by Item Report - Negative Lot Numbers

We are a food manufacturing company and must track all finished products by Lot Code. Our version of Quickbooks is the Desktop Enterprise Manufacturing and Wholesale Edition. We use the Inventory Stock Status by Item report to see total on hand quantity of each product. When we need to see the total amount of each lot code for a product we use the Lot Numbers in Stock report. 

The problem that we've had for over the last year is that the totals for these reports do not equal each other.  Here's an example.

Inv Stock Stock by Item report says we have a total of 10 units of product A.

The Lot # in Stock report says product A has the following Lot #'s in stock

Lot #23040403 - Qty 8

Lot #23040501 - Qty 6

Lot #23040701 - Qty -1

One report says our total is 10 and the other report says the total for the same product is 13. We can't have a negative lot # of an item. In the preferences pop-up we have always had the "Don't allow negative quantities" box checked.

I've reached out to Quickbooks support and screen shared with the tech 3 times over the last year for a total of about 9 hours trying to get the problem resolved. On every call we verify/rebuild data, reinstall Quickbooks, etc...

I'm posting here in hopes that someone else has dealt with this problem and might have found some solution. I'd prefer to stick with Quickbooks but at this point, we've begun demoing other software because our inventory in Quickbooks is so incredibly out of whack.