So i noticed something, the 404 that the software puts out causes some problems, i know this has been discussed before with 404 headers. Because i had a problem verifying my site with siteadvisor due to this.
Also Google webmaster will not recognize the file it gives you to provide ownership verification. e.g. mysite.co/googleedj893hd8nhd.html would be a 404 even though the file is there.