Redmond,
I saw you posted it a while ago, not sure if you still need help, but here are my comments.
First, it is weird that the pallet appears in the batch split. The batch split supposed to be the batches to the main item (the finished goods) and the pallets supposed to be a new item in the delivery, which can be manually included in the delivery and have a new item category for that.
I had a situation where pallets were in the delivery as an additional item and I did want to suppress this pallet from shipment cost document (and transfer freight the amount correspondent to the pallets weight to the main item) and I was able to do this in the SCD using the BAdI
Check User exit
V54KSFRC Determining the factors for apportionment of shipment costs
Check BAdI
BADI_SCD_ACCTG Call During Shipment Cost Account Assignment
Good luck
Leandro da Pia Nascimento