Site provisioned from WHMCS but not available in wordpress network list

Wordpress site is provisioned from WHMCS. It is also working fine.
Problem is, I cannot see it from superadmin interface inside wordpress.
It is not being shown in Network Site list.
A new user is created in wordpress but it is not associated with any website.
If I go to Pro Sites > Manage Sites and enter blog ID 2, I can see some details.