Right, the builder is meant to be used when you upgrade your hard disks. It erases them completely and lays down the partitions correctly. In theory, that shouldn't be needed on your player if it was working correctly for the original owner, but clearly something is up. The instructions for using the builder are in the disk upgrade guide.

You sure the thing isn't full of his music still? Look in all of the "trees" in emplode, open up all of the little plus signs.