I'm having some issue with this and Godaddy couldn't help and asked me to resolve it with wordpress.
I have 2 domain, my primary.com and secondary.com under 1 hosting account.
I created a folder under html root folder for html/secondary.
I installed wordpress 3.5.1 onto my secondary.com and loaded my theme in wp-admin and everything seems fine... Until I go to secondary.com and click on one of my category or try to read post. It would load my a messed up version of my primary.com with a note "nothing found for category xx"
Please help, been trying to resolve this for 3 days without any luck.