Why are commits to 7.x-master not included in latest versions of CiviCRM?
While Github is used for the code collaboration, co-ordination of which issues are fixed in which release is done on over CiviCRM's JIRA install.

In order to better ensure your PR was included in the next 4.6.x, you could open an issue there and tag with appropriate versions (eg 4.6.10 for fix version), then reference the JIRA ticket in the Github PR.