Shipments sent with tracking reappear as not sent and late

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I need to know what the deal is with this issue.  I use pirate ship and in the past stamps.com to send parcels. They are integrated and when I purchase the label for an ebay shipment then go back to ebay it shows as shipped with the correct tracking# added to that item.  A day or two go by and all of a sudden there the item is back on my "not sent" list showing shipment as late.. **bleep**  honestly, now if I go and manually put the number in again it seems to solve things.  I notice this NEVER happens if I ship through Ebay.  I am using the same carrier, going through my same post office. I am really **bleep** about the issue what is the problem???