If the reconcile isn't picking up any errors, then it sounds like the quantities in the database were inputted incorrectly. You would need to audit your SOP invoices in order to find the problems. Once you find the problems you can manually correct them and/or create an adjustment transaction to correct the quantity on hand values. You should ask your accountant which way he prefers you to do it because it will need to be reconciled at month/year end.
This does bring up the next question of whether it's a problem with the modifications. Does your add-in specifically affect SOP or Inventory transactions? If so, then you should get the vendor involved to see if it's a problem with the product or how it's being used. Also, if you don't mind telling us, what add-ins do you have?