Well just to clarify the issue with the patched security kernel, I test booted a vanilla kernel (2.6.20-mm3 with mm3 patches )
and the results were the same. Once I ran the script, the keyboard CapsLock LED would no longer toggle when I hit the CapsLock key. I'm not sure at all where the problem lies, there are kernel, and motherboard-bios differences, etc. I guess my point is, don't count on that ioctl script to work right for everyone.