Log in to eBay and go to Accounts -> Site Preferences.
Go to Selling Preferences -> Sell Your Item form and Listings and click Show on the right hand side. You will see eBay has moved the out of stock option to be a new site preference for you.
Can you confirm you have checked the box to use out of stock option from within eBay? If not, can you check that and hit save to update that preference? Ebay recently moved this to be a user preference.