What if a program required autoexec.nt to run? Would you then have to change the path in the new program to System32? The Autoexec.nt is a system file and should be kept where it is MrWhy has a safe idea of modifying Autoexec.nt check his threads out.
The way I read it, he is not deleting the file from the original location, just
adding it to the system32 subfolder/directory so I wouldn't think there would be a problem with other programs.