I dont know is it resolved or not and have you access to open the site in SharePoint Designer or not but I was also facing same issue and found below solutions:
http://www.learningsharepoint.com/2013/05/03/missing-save-site-as-template-for-publishing-sites-in-sharepoint-2013/

Hope this will help you.

I don't know is it resolved or not and have you access to open the site in SharePoint Designer or not but I was also facing same issue and found below solutions:
learningsharepoint

Hope this will help you.