Check whether you've created fiolder templates for those folders. If so delete them them by making them empty, after you've done so, the account template will be set for them.

Another possibility is that one/some of the recipients has an address book template set. They can be ignored by unchecking the option to use them

Folder templates can be found among the folder properties.
Address book templates can be found among the templates of the address book entry of your contact or in the the properties of the group your contact belongs to. Templates for a single contact have precedence over those for a group.