I put those scripts where no one is autorised. I've been concerned about this because I wanted to redirect first time users to a Flash Detection page. You have to make necessary efforts to ban both robots and humans from the folders where you keep those scripts. And if I can, I would recommend not to spoil your index page with such a purpose. The Home page is the most important page of a site.
Flash intros are the kiss of death for a site placement.
If you use Flash, use it as a complement to a complete HTML site, and please let the user decide what he wants to get. Yes - I agree about the use of Flash in this case. Bandwidth is not really an issue because the file sizes are quite small. I thought the redirect would be a good way of detecting the presence of the flash player whilst still giving spiders all they need in order to crawl the site properly and without spamming - the user is taken back to the original page after flash detection is successful. If they have the plug-in a cookie is set so next time they visit no detection is required i.e. the redirect does not occur.