A You have a meritorious defense to the shippers claim. You should insist that your drivers be allowed to place a shipper load and count notation on the bill of lading when you do not observe the loading, but the absence of this notation does not destroy your legal position.
Under the Bill of Lading Act, a carrier is not liable for the count when the goods are loaded by the shipper, the carrier does not know whether any part of the goods were received or conform to the description on the bill of lading, and the description of the goods is qualified by the terms shippers weight load and count, said to contain, contents or condition unknown or words of the same meaning. Sophisticated carriers use this statutory language to trump efforts by shippers to hold them accountable for shortage claims in the circumstances you mention.
prove a shortage claim, a shipper must prove (1) delivery of the goods
to the initial carrier in good condition, (2) damage of the goods before
delivery to the final destination and (3) the amount of damages. [Con-Air
Corp. v Old Dominion Freight Lines, 22 F.3d 529, 531 (3rd Cir. 1994);
Missouri Pacific R.R. Co. v. Elmore & Stahl, 377 U.S. 134, 138 (1964)]
Because your driver did not oversee the loading and the seal was intact, the shipper will have to prove through evidence other than the bill of lading that all of the alleged cartons were loaded on the shipment at time of pickup. Because the seal was intact at the time of delivery, the shipper will have a difficult, if not insurmountable, task proving that all of the cargo was loaded and that correct quantity was not actually delivered.
You also are blessed by having a clear delivery receipt evidence that you delivered the shipment intact and without loss or shortage. As a carrier, you should be skeptical of any count made after the consignee signs the bill of lading. The claimant will have a hard time convincing a judge that you are bound by the bill of lading count at time of pickup but that you cant rely upon the clear delivery receipt at time of delivery.
Finally, you mentioned that the shipment in question was shrink-wrapped onto pallets, yet the shipper has attempted to hold you responsible for a piece count. Even if your driver had been present at the loading, he could not have ascertained how many cartons were on each pallet. It is for this reason that drivers are properly instructed to sign for the number of pallets received said to contain the number of cartons shown on the bill of lading.