I know this is an old post, but I wanted to post my solution to this problem for reference as I couldn't find it anywhere. It's a graphical setting which is causing the issue. Open up the Skyrim Launcher -> Options -> Advanced -> Detail Tab -> Decal Detail (set to medium or greater). Apparently there is no Low setting for decals, only None, Medium, High, or Ultra. If it's set to None, then runes will be invisible.