Generic questions
Please visit http://www.packagekit.org/pk-faq.html for the most recent list.
Fedora specific questions
add/remove programs and gpk-install-file do not work when run as the root user!
GTK+ tools should not be run as root. Any GTK+ program run as the root user is a massive security hole -- GTK+ just isn't designed with this in mind. There are numerous attack vectors when running as root, and so we shouldn't be letting programs do such insane, insecure things.
PackageKit is fully compliant with PolicyKit, which offers easy authentication for regular user accounts to perform authorized system administration tasks like software installation. PolicyKit provides a dialog into which a user can provide the root password, and even hold this authorization permanently so the dialog is not required again later. Logging in as root is not necessary to install packages.
PackageKit won't work without NetworkManager
To continue using PackageKit without NetworkManager, either disable the NetworkManager service, or edit /etc/PackageKit/PackageKit.conf and change the following value:
UseNetworkManager=false
PackageKit won't work with my proxy server
Short answer:
If you set this in the "Network Proxy" capplet in GNOME then it should just work. If you need to make manual changes then change the values in /etc/PackageKit/PackageKit.conf.
List of issues filed
For a list of PackageKit issues, visit this link.