It is possible that the problem is related to the alpha software, I had major problems uploading tracks with emplode when trying it. Unless you need to play Ogg or Flac files, I recommend using 2.0 software.

In the meantime, look at these:

checking disk integrity

Manual disk checking

rebuild databases

disk trouble


Finally, since your hard disk is 100 gigs, it could be related to the drive having not been "built" correctly in the first place. If none of the above things help, then try rebuilding the disk from scratch using the most recent versions of the builder, kernel, and player software for large hard disks linked from the drive upgrade guide.