none of these workarounds worked for me either (Kubuntu Jaunty), but then I did the following:
1) in confizconfig settings manager, keep gnome compatibility enabled, but change the two keybindings to something unused in KDE (I chose <alt><super>F6 and <alt>F6).
2) In System Settings > Global Keyboard Shortcuts > Run Command Interface, verify that <alt>F1 and <alt>F2 still map correctly.
3) Log out, and log back in.
Now both <alt>F1 and <alt>F2 work as they did before I installed Confiz.
none of these workarounds worked for me either (Kubuntu Jaunty), but then I did the following:
1) in confizconfig settings manager, keep gnome compatibility enabled, but change the two keybindings to something unused in KDE (I chose <alt><super>F6 and <alt>F6).
2) In System Settings > Global Keyboard Shortcuts > Run Command Interface, verify that <alt>F1 and <alt>F2 still map correctly.
3) Log out, and log back in.
Now both <alt>F1 and <alt>F2 work as they did before I installed Confiz.
hope something works for you!