Inventorying an incoming pallet simply isn't as easy as reading the manifest. You have to physically check that the contents of the pallet match what is on the manifest or you will have stock loss (and lost money!).
One major area of stock loss for many companies is transit. Either the company who shipped the goods didn't manifest them correctly, or they accidentally shipped the wrong goods, or stock was misplaced or stolen while in transit. When you receive an order you need to count what is actually on the pallet against what is on the manifest and then have another person verify this. Depending on the goods, this can take time. Big jugs of milk - easy. Clothing, small domestic appliances - not so easy. Items like small TVs, mobile phones, laptops, game consoles, MP3 players and cameras are all high-value, low-profile, and easy steal goods that need to be physically counted at easy stage of transit.
After this you still need to have someone (usually a clerk dedicated to this task) add the goods to the electronic inventory of the receiving company, raise discrepancy issues, etc.
I've spent ten years working in inventory, and I'm currently the inventory specialist for a national company. RFID tagging is an excellent idea for tracking stock movement and Wal-mart's initiative into this is ahead of it's time. RFID will be way that all stock control will go in the next decade, but it will never replace the need to physically inventory goods. Their charge for the both tag and labour on Wal-mart's part is actually pretty reasonable, but it only tracks pallets and not the goods on them, which is what is important for companies.