I have Powerquest Boot Magic installed on my MBR. The first time I asked kdm to reboot the system, it gave me a list of the partition I could reboot do from the lilo.conf file. But simply rebooting back to the standard MBR did not appear to be an option. After selecting a DOS paritition that I really wanted to, the system rebooted and then hung. After a ctl-alt-del reboot, I ended up booting strait to the linux partition, Boot Magic no longer was functioning. After several attempts to put things back together, and reinstalling Boot Magic, the (DOS) BM configuration program still isn't working correctly, and there some as yet undetermined amount of damage to my disks partition tables. I'm working with Powerquest support to try to determine what is broken and whether it can be recovered. In the meantime I would warn people not to use the kdm reboot feature under any circumstances.
If you aren't using LILO, don't ask kdm to configure LILO for you. Open kcontrol, go System > Login Manager > Sessions, then deselect "LILO > Show boot options". You'll lose the feature of being able to specify which OS/kernel you want to boot next time around because this doesn't work with any non-LILO boot managers.