bppcfix has a couple of options. I personally use:
"c:bppcfix install 040 reboot" in my startup-sequence.
It will basically remove the onboard ppc.library in the bppc card
as well as the 040 one and will reboot if it had to do the change,
Otherwise, it will just continue to boot if it didn't need to change anything.
If you run it once in workbench, to make the changes work, you
will need to reboot the machine. Either manually or via the reboot
option as above.