Issue Non BOM item for Shop order

Hi Friends!!
BPCS Version: 6.0.4 (now migrated on 6.1.01)
Plateform : AS400

If we issue one item (which is not defined in BOM) against a shop order as an
Alternate to an existing BOM item,  through INV500. This program insert a line
in FMA for this new item showing Qunatitiy Issued xx, also make the standard
required Quantity xx. This standared required Qty makes problem at the time of
CST270. Because this report shows the total Standard cost for all material. It
will include both required qty for both items, the BOM item which is not used,
as well as the alternate item which is actually used. 
Please note this practice is so frequent in our industry, that we cannot
afford to change BOM all the times. 
Can somebody give us the idea how to keep the standard quntity as it is
defined in BOM!!!  

Thanks
(Adnan)



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