I have the exact same problem. I've found that MusicBee is putting all of my music I am syncing to my iPod into the partitioned/root folder (which I didn't even have activated!). You should be able to find all of your music by navigating to your iPod in Windows Explorer.
Anyway: How does one sync their iPod (in my case iPod Classic 120gb), so that their music actually displays and plays on the iPod?
Edit: After much reading on the MB forums, I realise now that MB really doesn't like newer versions of iTunes. Does anyone know which version of iTunes works best for syncing with MusicBee? Or even better, which is the best way to get MB to sync without iTunes installed (and preferably, a way to sync without having to use a separate program?)