Aah, ok now I got your problem. This is a known issue.
You should have formatted your hard disk through the slugs webinterface to avoid this. Now you have to create some diversion scripts to avoid the automount-failure. :-/
So, just to clarify, you have one ext3 partition on your HD, but 2 ext3 parts on your usb stick? Workaround is to copy all the /opt directory and whatnot gets linked to the usb stick to the HD.
Anyhow, if you can find the right script to divert from, it should be easy to unmount the HD and remount the flash’s /conf partition to the correct location.
The nslu2-linux wiki should provide all the needed info iirc.