there could be two things, i can think of. one is that in the autoimport options of the map 'ignore files previously deleted' is selected.
an other option is that those files are already imported but under the wrong media type (for instance data).
to check this, make a smartlist, as a rule try media type is not audio, and see if you find the files you are missing in mc. if so, select one of those files, go to tags, show all tags, and change the media type to audio.
succes
gab