Hello Everyone -
The issue is at the time of creation of sales order. If the sales order is enetered with VA01 and both the ship to party and sold to party are keyed in the respective fields. The system just checks for the availability of the customer in that sales area. But it overrides the assignment of the ship to party in the customer master.
I remember this was a long pending issue in 4.6C.
But there is a SAP note which triggers a warning or error message when the user "keyed in" different ship to party customer that is not available in the "Sold to party" customer master assignment. Unfortunately, i could not locate it now.