Discrepancy between Physical inventory (Calculated) and Quantity on hand

On the Physical Inventory journal, when we run the Calculate Inventory batch 
job, the quantity calculated and displayed in the 'Qty. (Calculated)' field 
does not match the 'Quantity on Hand' field for the ietm. The difference is 
the Physical inventory adjustments we have posted during the previous 
physical count and for some reason, the Calculate Physical Inventory batch 
job doesn't seem to be factoring in the physical inventory adjustments posted 
previously through the physical inventory journal. Has anyone seen this 
before? How can we address this?
We have run Adjust Cost batch job and have automatic cost posting to GL 
turned on.
Thanks a bunch

Are you using advanced warehouse features?