Inventory Stock Status Report vs. Physical Count Variance Register

We are currently using MAS 200 for inventory reconciliation.  I use the stock status report to balance our physical counts to MAS, giving us a potential variance amount.  Once I enter the physical count numbers into physical count entry I am finding that the average cost on the Inventory Stock Status Report is not matching the average cost on the Physical Count Variance Register, is anyone else having these issues? 

Thank you,

Jenny