There's a few situations where eBay orders won't show up in Pirate Ship:
Pirate Ship only imports Unshipped orders. If your order has already been marked as shipped in eBay, it won't show up.
If you bought a label in Pirate Ship and refunded that label, we are not able to re-import that order. You'll have to recreate it manually.
Pirate Ship will only import orders with the financial statuses of Paid or Payment Pending. This can be configured in Settings > Integrations > eBay > Edit. If your order has a different status, it will not be imported: