I don't know why it'd say the program doesn't exist - it obviously does, according to my script.
If the program is named "startup" it will run when the computer turns on, otherwise it will not.
You should be able to terminate out of the program you posted, there was nothing preventing it. At a guess, I'd wonder if you didn't hold down control+t long enough (the time varies).
There is a flaw in your logic, though this shouldn't cause what you are experiencing:
if input == "S" or "s" then
Will always be true, because 's' isn't nil or false. This is mainly due to your misuse of 'or', the correct way would be this:
if input == "S" or input == "s" then
If you want some advice, I'd use string.lower.
if input:lower() == "s" then