I seem to remember this happening to me with an earlier version of gnucleus (hasn't happen for a while.

It was to do with the file names and the second bracket after the keywords. look at the partial files and if the closing bracket isn't there put it in and gnucleus should see the files again.

File names should look like

Name or file(size, keywords).file_extension

eg.

Frank Sinatra - My Way (4452280,my way frank mp3).mp3