That's because the message is not related to permissions, per se. It's related to older files on your system that have permissions attached to them that are no longer in use in the new Disk Utility. So they are flagged as an error. They may also be permissions your have set that are not recognized.
Were you to erase your drive and reinstall Snow Leopard from scratch then repair permissions most if not all those messages would disappear and be replaced by another set of repeating messages that were never fixed in Snow Leopard. 🙂 I do believe, however, that once you upgrade to Lion or Mountain Lion those messages will all disappear.