I have a SharePoint 2013 publishing site collection that has a custom master page for look and feel. I created a site template (also a publishing site) that inherits the master page from the parent. When I create a new subsite using that template the master page doesn't take effect until I manually go to Site Settings | Master Page and flip the radio buttons from Inherit to Specify and back. Why?
You can do this by editing the onet.xml inside the solution file. You will have to extract the .wsp from the solution gallery then edit the onet.xml so that the master page urls looks like this:
note the first slash!!!
then use makecab to create a new cabinet file.
Browse to the master page settings, check off the box that says "Reset all subsites to inherit this site master page setting", and click OK.
A similar question has been answered here: How do I get a subsite to inherit the main masterpage?