You Queued the Auction lots for listing before they had ended? Did you change the Auction lot status manually as they cannot be Queued for listing when the Status is Online?
If you wait a couple of minutes before using Auction Site | Update all lots, after the auctions end, it will work better. It is an eBay issue not an AW2000 to wait. It is the way eBay releases information about closed Auctions.
So wait just a couple of minutes when the End of Auctions come in before updating all lots.
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