PackageKit's software update, by default, has packages that are on hold checked for update. It shouldn't have them selected, or otherwise an user might update a program that he/she doesn't want to. For example, netatalk in my computer is on hold, because I built it from source for encryption support. Ubuntu's netatalk does not have encryption support, and I put my package on hold so that Update Manager does not update it. It appears greyed out in Update Manager, but will appear checked in Software Update.
This bug report is very old and based on a version not supported anymore. By upgrading to a newer version of PackageKit you could receive bug fixes and new functionality. You may need to upgrade your Linux distribution to obtain a newer version of PackageKit.
Please feel free to reopen this bug if the problem still occurs with the latest version.