If you see the "Publish Order Settings" link under the Order Settings column of your Store Manager, that indicates you have made changes to the column that have not been published. If the changes are not published, then they would not be reflected in your live Yahoo! Store.
After making any changes to this column that you wish to affect your store (such as creating a new shipping rule), click the "Publish Order Settings" link. When the changes have been published, this link will change to say "Published."
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