Matt: I've provided some repro steps to the dev team - they will be looking at what sounds like a Windows shares' only issue.
Meanwhile - just in order to gather more info - would you be willing to put the exact same folder structure and files you have on your windows share (or part of it) onto an USB key, connect it directly to the Rasp and play the same set of tracks and see if you get the correct (i.e. the one embedded) displayed in RuneAudio's main page?