LinuxPPC 2000, or more specifically, bootx has had this problem ever since 9.02 came out. That is the version of the OS that shipped on new Macs for the last 2 months.
There are a couple of options to get around this. Read the suggestions in the mail list about setting up a yaboot.conf file and using yaboot on your primary MacOS drive. I have this setup where to boot into Linux, you hold the space bar dowen as you turn on the machine, the computer then boots straight into linux. If I want to use the MacOS I just restart Linux and it will then boot MacOS.
The arrangement works with 9.02-9.04.
It is a combined problem with BootX and the new MacOS Rom file that shipped with these versions of the OS.