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So what about all those songs that showed up? They don't show up on the player.
Right because they are not supposed to be there. The empeg doesn't store its songs as loosely named MP3 files like that. It stores them in a completely different way. Someone who had the player before you filled up its hard drive with loose songs that you'll never be able to play.
They either didn't know what they were doing, or they were doing something nonstandard like running some other kind of player software. Either way, you're not going to be able to use those hard disk(s) in that state. You must wipe the drives from scratch, by partitioning and formatting them with the builder images mentioned in the Disk Upgrade Guide at riocar.org.