I have not yet installed AppleJack, since I'm a little nervous about it, but I extracted the archive so I can look at the shell script.
The script does not currently look to see if it is in single-user mode or not, and the docs I read said that it must not be run if not in single-user mode.
I wanted to suggest that AppleJack check it's current runlevel with
. run-level 3
I can be reached at rlaska a-t g m a i l d*t com