Residual Inventory Cost

I have a client who sells inventory before it is brought into stock, so they frequently end up with negative values. They are getting the situation where once the inventory gets to zero, they get cost balance left. i.e. zero quantity on hand, but as residual cost posted to inventory. They do run the adjust cost program. We are having trouble getting the cost against these items back to zero. This affects the inventory valuation. Does anybody have any ideas of how we can rectify these balances? Client is running V5 SP1