Did you add any steps to mount the system? I don't believe I did, but it seems others are finding it to be read-only.
I did on a mac and for whatever reason, once i did get the # for root term (even after you get $, WAIT people. It WILL return you to native command line), if I exited, it wouldn't be root anymore so I had to just copy the files to sdcard, manually remount the system (i just did "mount -o remount,rw /system /system") and then copy su, superuser.apk, and busybox into their locations.