First, You would need to identify the type of site. Is your site a
publishing or non-publishing site. If you recall, in the interface of
the browser you actually have two setting that allows you to manipulate
the settings associated with the master page.
Second, I am making some assumptions here, you would need to ensure that
the inheritance of the master page has not been changed. That means
that a site owner has not chosen to specify their own master page at a
specific site.
Generally when the Site Master Page settings are changed and forced to
the lower level sites, your newly created site will use the new master
page settings for all newly created publishing sites. That is due to
the publishing features. In other words, the newly created publishing
sub-site points to the Master Page Gallery hosted by the Top Level site.
On the other hand, configuring the System Master Page settings and
reseting that configuration for the lower level sites only affect
sub-sites that are created. After creating a sub-site that doesn't use
the publishing features, it uses the master page (default.master) in its
local Master Page Gallery. That behavior is by design. In the event
you want to change that behavior, you will need to programmatically
make that change.