Hello JavaDragon,
Due to the overwhelming popularity of the Humble Bundle promotion, we ran out of our current stock of Beginner Boxes within the first 24 hours. Yours was placed after we had run out. We contacted Humble Bundle and a notice about the backorder was placed on the promotion page, which indicated that our reprint is estimated to arrive in late June/early July. Once that reprint arrives, we'll be working as quickly as possible to ship Beginner Boxes out to folks who purchased them through the Humble Bundle.
The "2 to 5 business days" estimate in the "Shipping Method" portion of your confirmation email refers to the transit time to your selected address for this order. This estimate is not an indication for when the package will be leaving our warehouse. However, once we do ship your package, you will receive an shipment confirmation email that the package is estimated 2 to 5 business days to make it to you.
Charges for Shipping and Handling on your Beginner Box order are not finalized until it is processed for shipping. You may have seen a temporary authorization on your card for the shipping cost when the order was submitted (it varies from bank to bank if they display the authorization or not). Because it was not finalized on our side, it will expire from your account. That charge will be processed when we process it for shipping in the future. More details about billing and payments on paizo.com can be found in this post in our FAQ.
If you want to check out the contents of the Beginner Box before your order arrives, all of the player and GM materials are available for you to read in PDF form on your My Downloads page.