Ideas

The rate in INVSTOCK for GRC & GRT is different for local outright stores. 

Suppose a transaction of Item with Qty. as 1, where Basic rate = 100, Charge amt = -10 & Tax amt = 15.

GRC:
The formula for inserting rate in INVSTOCK is -
When "Include Tax in Cost" = Yes (inter-state), then (Basic Rate+Charge Amt+Tax Amt)/Qty. In above case, its (100-10+15)/1, i.e., 105.
When "Include Tax in Cost" = No (local), then (Basic Rate+Charge Amt)/Qty. In above case, its (100-10)/1, i.e., 90.

GRT:
There is no differentiation for inserting rate in INVSTOCK depending on "Include Tax in Cost".
The flat formula is (Basic Rate+Charge Amt+Tax Amt)/Qty. In above case, its (100-10+15)/1, i.e., 105.

That means for inter-state both GRC & GRT rate is reconciling but not for local sites. Need to reconcile the rates.