I got rid of the restore bootcode and removed sudo from the line in bootlocal.sh - but that didn't help.
I then thought that maybe my root password was getting in the way so i removed etc/passwd and etc/resolv from .filetool.list, rebooted, tried again, rebooted, and eth0.sh still was not maintained.
Then I listed mydata.tgz and discovered that eth0.sh was not being backed up, even though I was telling it to.
At that point I went into .filetool.lst, deleted the /opt/eth0.sh line, and readded it. That seems to have worked now.