I recently moved my website from staginga.certain.com tohttp://www.certain.com. Running 5.6.0.2

I've noticed that my 404 page only comes up when incorrect pages after index.php/ are added.

Example:
WORKS AT - 404 will show up forwww.www.certain.com/index.php/adf...
DOESNT WORK - 404 will not show up athttp://www.certain.com/daf

I went into the config/site.php to see if everything was correct and it is.
Went into config/site_theme_paths.php and put it as my theme "bootstrap" which is correct.

I just don't see why its not acting correct? Any suggestions?