Every time I set the permissions for /usr/bin/apm and /dev/nvram they revert to what they were after I reboot. Any ideas as to why that might be happening?
I would suspect that udev or devfsd are changing them back. To check your devfsd stuff you can look at and edit /etc/devfsd.conf - in udev it's a little different, you have to create a file in /etc/udev/permissions.d that will have the permissions that you want to override. If you name it 00-udev.permissions it will take over from the base udev.permissions.
This might help: