Creating Multiple Pack ID for a Single Sales Order Release

We are a Multi-Site company on E9 702A and we have 2 locations that primarily supply 2 customers, which provide us blanket PO's for the year. both sites currently are in the practice of making multiple pack ID's for a single release on a sales order, sometimes multiple packs for the same sales order release on the same day. Now we are noticing that back order quantities are not accurate, sales orders are not closing out the release when the full release quantity has been shipped, and occasionally, a message pops up stating "the sales order is allocated in another location" and prevents any further shipments on the sales order release. Does anyone else ship multiple pack ID's on a single sales order release? If so is there a way avoid these issues?

 

Thanks

-Phil