Sounds like the files got uploaded but the root playlist didn't. You should be able to nuke the files from jEmplode. You'll need to either create a 'soup playlist' that shows all tunes or better yet do an advanced search for 'refs=0' which will show you all the tunes that are not attached to any playlist. You should then be able to select them all, delete them, and sync to get them off your player.

Once you get rid of the files that are already on there you might want to start by adding a root playlist with just a few files as a test to make sure everything works OK. I have synced 20+ gigs with jEmplode more than once under OSX, but I think I always started with a partially populated empeg.

-Mike