Thanks Basara. I may have not replied to you in the rush but I sure go through all replies

. Indeed your previous inputs did help me resolve my previous query. But this issue seems to be unique. Here are some snap shots.
1. I am attaching snippets of the Cpanel showing my subdomain. This was configured a month back and no issues from server end.
2. The Cart Admin settings
3. The cart with url issues
4. The cart with url issues resolved. Amazingly this happens every time I manually press save settings in cart admin panel.
The permissions have been set properly in the server too.
On the other note I also spotted that the Softaculous records in my cPanel show the old url. Could this be the reason? I have amended it now. Not seeing immediate changes yet but keeping my fingers crossed.
*** UPDATE ***
After amending the installation records I accessed the cart admin panel using the subdomain url. Now every thing seems to work fine. (So far so good

I think I had amended all the settings but was still accessing the admin panel through main domain url which was causing the unique issue. Only time will confirm how the new amendments works. Will keep the forum updated.