You have to run "Repair iPod". Its not helpful that Yamipod immediately quits on any error.

1. Move Yamipod to your desktop if you're running it from the iPod like I was.
2. Disconnect your iPod
3. Open Yamipod, select Tools > Advanced > Repair iPod
4. Now connect your iPod and go through the steps to repair. You'll lose a bunch of junk but at least you don't have to reinstall iTunes if you s**tcanned it like I did.
5. Everything should work now.