(On Debian Wheezy with KDE.)
I believe it's better when update settings can be set globally by the system admin in some /etc/ file. Using /home/<user>/.kde/share/config/apper for thing like [CheckUpdate] autoUpdate=0 isn't the right place.
I think you need to get the apper author to submit a patch to add the settings to /etc/PackageKit/PackageKit.conf if you want some kind of user default value.
We moved the upstream bugtracker to GitHub a long time ago. If this issue still affects you please re-create the issue here: https://github.com/hughsie/PackageKit/issues
Sorry for the impersonal message, and fingers crossed your issue no longer happens. Thanks.