No - you are right. rpm's are installed but /usr/lib/pkgconfig/ndesk-dbus*.pc are missing.Are you sure you installed ndesk-dbus and ndesk-dbus-glib correctly ?
uninstalled rpm's and reinstalled manually from http://fedora.secsup.org/linux/development/i386/os/
./configure now complained about unknown URL keyword in usr/lib/pkgconfig/ndesk-dbus*.pc
removed the URL line in usr/lib/pkgconfig/ndesk-dbus*.pc files ./configure now succeds but it does not compile. I will move this issue to ANNOUNCE: Beagle & Libbeagle 0.3.4 thead/knr