but I am interested in this question. As I know, the purchasing cost should include the unit cost and freight cost, so your system did not include freight cost into inventory cost, which is not correct. This question should be solved by IT department.
Another difference about exchange rate, I do not know if you do monthly (profit and loss accounts) and quarterly (B/S accounts) exchange adjustment. If you do it, exchange difference will be solved periodically.
The last difference about input delayed by workers, I think this difference is temporary and will be solved in the long run. But you still can adjust them in the short run to make it balance.
Not sure if the above make any sense.