I have prime 2 day shipping and did not change my order in any way for the LE. I was pissed about the delivery date for my regular edition order being a week after everyone else (even with prime shipping) so I called and they bumped it up. After reading here about how modifying the order will set you back, I made sure I didn't touch the order for my LE. Yet, I saw on here that for both books people who ordered last got theirs first! Total BS on Amazon's part!
Did you make any changes to your payment method? If you do anything like that, then your order gets moved to end of the queue. Meaning if your were the first person to order and a total of 1000 people ordered, and you made a change later on, then your order will automatically become the 1000th order (while everyone else moves up). That might explain why. I'm not sure if other changes (like quantity or address) effect this.
What shipping method did you choose? If you have Prime or you paid for standard shipping or anything faster, it will usually bump you towards the front of the fulfillment line, but you have to choose the faster shipping at the time you order. If you modified the order in any way after you placed it, such as changing shipping address, speed, or payment information, your order falls to the back of the queue. At the end of the day, it looks like Amazon just plain oversold. They had the limited edition listing up before Dark Horse announced that it was limited to 4,000 copies, so they were probably taking orders before they knew their exact allotment.