It's not just the shipping that makes the difference; it's also the warehousing of the items.
As a seller, you don't just leave your items lying around after taking pictures of them for your listings. You weigh them, make sure you have a proper box for them, note as much relevant information as you can in "item specifics" and so on. You have your ducks in a row so that you can get the item packed up and mailed off to the buyer as quickly as possible.
When an item is carried by or warehoused by Amazon, it also has all the information it needs at the ready to get the item packaged and sent off as quickly as possible.
When the eIS hub receives an item, it may or may not have enough information from the seller to get the item prepared for exportation immediately. The variables aren't controlled the way they are with a shipment you or Amazon may be making.
Some of this may be the fault of some sellers. I get the impression from the posts on the eBay.com discussion boards that despite eBay's attempts to educate sellers on eBay International Shipping, there's still a significant number out there who don't know the program exists yet are opted into it or don't know how to use it properly, and this causes delays and problems if their items go through the eIS hub. Some of this may be the fault of the design of eBay. eIS can't really do much to pre-vet listings except record the item's category and the item specifics, and what information is in the item specifics may not always be enough for customs purposes. Also, I wouldn't be surprised if the eIS hub has seen significant staff reductions since the program was rolled out.
On the other hand, Amazon's shipping service is apparently a money-loser for the company, which shouldn't be too much of a surprise. Pitney Bowes' e-commerce/logistics division has recently declared bankruptcy, after all. What analysts can't figure out, however, is if it's supposed to be functioning as a loss-leader or if it's a financial drain on the company.
