sub-domain page URL

I have 2 independent instances of WP running i.e the main website and for a sub-domain. The problem with the sub-domain pages is that they seem to show up as sub-pages of the parent domain and not the sub-domain.

Open the below website:

http://portal.mindsharehr.com/

If you click on any link in the menu, the URL changes to something that looks like its part of the parent domain i.e http://mindsharehr.com.

For example, if you click on the home icon, the URL becomes

http://mindsharehr.com/portal/

If you click on any knowledge center topic, the URL becomes

http://mindsharehr.com/portal/strategic-hrm/

instead of

http://portal.mindsharehr.com/strategic-hrm/

Can somebody explain why this is the way it is and how to fix it?