Comment 40 for bug 346788

Alright all you 9.10 users here is the fix. Be aware that there are 2 levels of security that you are going though.

First part has been done for you #21 and all the others get the credit here by doing:
After lines:
    def __init__(self, *args, **kwargs):
        super (MainWindow, self).__init__ (*args, **kwargs)
        Master.register(self)

and before lines
        self.denormalized_virtual_hosts = {}
        self.plugin_manager = PluginManager()
        self.apache = Apache2()

insert lines:
        # HACK : work around bug @see https://bugs.launchpad.net/rapache/+bug/346788
        if not Shell.command.ask_password(): sys.exit(1)
        # HACK END

Second part is: sudo gedit /usr/share/applications/rapache.desktop
Change line *** 5 ***
[Desktop Entry]
Name=rapache
Comment=Simple tool for managing and configuring an apache2 instance
TryExec=rapache
Exec=gksudo rapache
Icon=/usr/share/rapache/Glade/icon_cadsoft_eagle.svg
Type=Application
Categories=System;

Then reboot, please just reboot. When you access rapache in the system menu you will type root password twice. Then it works.