Actually, from your description it sounds like that it only detects a save that has a game installed. It's not a matter of disc or not.On the list of detected WiiU saves there are games missing, every game that requires a retail disc is missing (there may be others but I don't think so). Having turned MK8 into a an installed game via disc2app and wupinstaller its save is detected, though I had loaded it and then had an autosave before I tried using savemii so I don't know at what point that changed, again I'll check when I get back. This happens with every version of savemii I've used.
I haven't had a chance to use the program yet so I'm not sure if it's normal behavior or not, but yeah that's what going on