I am surprised that you're having such difficulty with the iPod on MC, it's really well built, IMHO.
Rather than manipulating the playlists
on the iPod I would like to suggest manipulating the playlists
within MC instead. For instance:
1. Start from scratch again by using MC's "format iPod" option on the right-click. If this works, you won't have to do this all the time anymore, I promise,
2. Go to the Playlists tree node in your media library. Not the Playlists node that's a subnode of the iPod, but the one that has all the playlist groups in it.
3. Make a quick playlist. Just a couple of songs.
4. Go right-click the iPod again and select "Synchronize"
5. When the sync dialogue opens up, click "Select None", which will de-select all of your playlists; just in case they were selected. Now go find your quickie playlist that you just made, and put a check in the box by it.
6. Before you hit "OK" make sure that the "Delete files not in list" and "Update tags" boxes are checked. You can use "Auto Sync" if you like (it will bring up this dialogue every time MC starts if your iPod is connected... mebby do that later)
7. Hit OK and see if it transfers the music. Once you dismount and unplug your iPod, it should have a playlist on it that's identical to the quickie playlist in MC. Now, build a lot more playlists and smartlists and enjoy!
The key here is to get all of your music "looking pretty" in MC's media library. The plugin will only transfer music that's in your library, so be sure it's all imported and tagged properly. Have all the "artist" and "album" and "name" and "track number" fields filled out as a minimum.