multlple pack configurations on o/e sales order for single item

need some insight. we have a customer that is ordering a single item, but has varying pallet quantities. Ex. sales order 1 has pallet qty (pack qty) of 312 pieces, and a total item qty of 3432. Sales order 2 has pallet qty of 218, and a total item qty of 2398 pieces. My whse has practically refused to scan, so we set the customer as Autopack to print the appropriate number of lables prints based on calcualtions from the picktickets. Doing it this way requires that we have multiple items set up in the item master and in the EDI ASN Bulk Weight file. Question, does anybody know a better way to do this? I ask because as an EDI Customer, this causes significant issue on the EDI end.