Please forgive my panic stricken post...If I would have just breathed I would have realized I had this exact same issue last time and Alex solved it immediately for me. I apologize. here is the answer to this issue from Alex:
The Autotune Error Checker doesn't currently follow redirects. So, if you go to your admin site at
site.com/administrator, we'll check
site.com. However, if the main site is set to redirect to www (like
www.site.com), then you should access the admin area as
www.site.com/administrator so that the Error Checker will be checking the www version of your site.
We're working on re-enabling redirects on the Error Checker, but we ran into some issues with it. If the above doesn't work, just let us know!
Thanks,
Alex