Ok, this is weird.
It is my understanding that if a file is not in my template directory the next stop is the default directory. Now I know from the docs that single.php was the file that should have been the file I needed to edit which was edited in the default folder.
So I took that exact same file and saved it into my template folder and bam now its using it. So there is no longer an issue but man that was driving me nuts, why did it not see that file in the default directory? The world may never know.
Thanks for the response though, the url must remain a secret now, simply because its a real mess. Heh.
Thanks anyway.
J.