Not all groups showing in Site Permissions page

Hi,

In my site collection, I can see many groups which i created in Site Settings ->People and Groups (_layouts/groups.aspx). But all these groups are not showing/listed in Site Settings-> Site Permissions page (_layouts/user.aspx). Instead it list very few groups. Because of this, I am unable to check a group's assigned Permission level. I have applied a custom master page for my site collection.

Regards,

Naush