Stranger and stranger
I went back to check the index file and they were not updated when I loaded the file. I thought that this was strange because the file size and date changed. I deleted the index file and reloaded it and it worked fine.
So, now my question is do I need to manually delete the index file for each new site? The FTP program that I'm using is configured to over write files and I was never prompted to delete or over write.