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MRP run for all planner codes


I am having a problem with some items not running correctly during Run MRP for All Planner Codes. The problem is that more often than not, we find some parts that are not run correctly after the run is complete ( ERP is not creating necessary planned PO or WO according to demand therefor availability goes negative). This issue for individual parts can be fixed when we run MRP by the only those items. However, we keep finding different individual parts not run correctly when we run MRP overnight or over the weekend. We usually run MRP 2-3 times one after another in by using Xtuple connect in Windows virtual machine.

Is there anything we can do to fix this issue on our end?

Thank you for the help in advance