I have 3 domains (a.com, b.ca, c.ca for example) on the same GoDaddy hosting account. I decided to move the two sub-sites to separate folders. Since I did this I can access one of the sites (b.ca) with its domain name but the other site only works properly if I access it using the primary domain (a.com/folderc). If I access it as c.ca it displays the home page without a theme and any links do not work ... if I attempt to link to another page from this home page, the link is c.ca/folderc which is incorrect.
To complicate things all of the DNS entries are being handled by Fastmail. Fastmail has both sub-domains using the same IP address for the A records ... I think that GoDaddy is then directing to the correct sub-directory but perhaps there is something going wrong there.
I've looked at both sub-directories .htaccess and also settings.php and can't see any significant differences. What am I missing? Is there something in the MySQL database that affects this? (I duplicated the database changing only the database name and anything referencing the database name but since I can access the site using a.com/folderc I'm inclined to think that there is nothing wrong there.)
Clearly I am missing something. Any ideas what?