Also, you may or may not know you can just copy the config files over from the CONFIG/FROM to the CONFIG/TO directories if you are doing this on Windows. Lastly, since you said you were using cgminer, it has been my experience to skip FIX# 20.
Oh nice thanks that will help later when I have to remake the images.
Also I think I found the solution to my problem: use the -f switch to coldreboot and shutdown ("coldreboot -f" and "shutdown -hf now"). This forces the machine to power off/cycle. It's not clean, but I figured that since BAMT runs off memory it shouldn't affect much. I could be wrong.