I edit a master page with SharePoint Designer, then I save changes and then I close SharePoint Designer. When I open that master page again, the last changes don't show up.
I had this same issue. After i made a change to a custom master template, saved and checked in then re-opened all changes had disappeared. I found the actual changes were being applied and visible on the webpage.
The issue appears to have something to do with the local cache in your profile. Clearing this resolves the issue.
Delete the data here: