Physical Inventory

Our Inventory Valuation Report and Trial Balance do not match the value on the Balance Sheet (the Balance sheet value for Inventory is higher by a significant amount).  I have seen the knowledge article for the reasons for the delta between these two, but wanted to ask if items with negative inventory values are not taken into account on the Balance Sheet, but are taken into account in the Trial Balance/Inventory Valuation Report?

I would like to reconcile these two, but need assistance and to narrow the possible reasons why the delta occurs prior to performing a physical inventory.   We are on average cost. 

I believe the Negative Inventory Tier report is not used with the average cost method.