MPD scan doesn't find tracks (flac's in my case) properly when CUE or M3U files are in the same directory. When CUE and/or M3U files are removed MPD scan find files properly.
I've just tested it on the system at current state of development (0.3-alpha) and I don't have such a problem, maybe I already fixed that. Could you test with another client (MPDroid or GMPC) to see if you notice the same behaviour?