Why won't my order show up in Pirate Ship?
Is it a Global Shipping Program (GSP) order? In that case, you can only create the label manually. Read more about shipping GSP orders here.
Is the order status Paid or Pending Payment, or has payment been held? Read more about eBay payment statuses here.
Why won't my eBay order go away?
Is an order you've already shipped or a cancelled order showing up in Pirate Ship? Read more about eBay's issues with old orders here.