Has anyone implemented Project manufacturing instead of ETO and interfaced with Job Cost via flex ac

We run into a problem with Project specific items in our current ETO/Job Cost prototype once a PO is received and the items are put into inventory, SInce the inventory detail records are not "striped" with the project number, the MRP may suggest allocating this project inventory to a different project as it just processes requirements in due date order against inventory on-hand, even though this was purchased by another project/job and was already burdened to that job. Then it would also generate a buy message for the project that you had already purchased the  inventory for, doubling the cost