MadTechie

Hi oymediasolution,
I am assuming that WP or another system is installed some (another domain) the problem is these share the folders, it doesn't matter if its another domain, that only see the folders,
if the add-on domain inside another domain? (folder wise)
for example, 
/public_html <- main domain
/public_html/new_domain <-addon_domain
if this IS the case then it maybe worth looking at the main domain and checking if the same .htaccess file exists 
if so then you should be able to create a addon domain at the top level instead, this MAY solve the problem e.g
/public_html <- main domain
/new_domain <-addon_domain
Lets us know your findings and i hope this helps