Larry
They are set, but Pat here may have hit on something.
1. I have 2 / (roots) 1 @ /dev/root which is loading and 1 @ / for /dev/hda3
2 I seem to be booting into /boot @ /mnt/.init.d not /boot on /dev/hda1
Not entirely sure I understand this "two roots" business :) but could it be a bootloader issue? If you use grub, you might try mounting /dev/hda1 to /boot and look at grub.conf to confirm you've got things set the way you expect (e.g., the root line, and the root= argument to your kernel line for loading Linux).
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