I remember that this used to happen to me also when I had my 4G iPod Touch, though I cant' remember if it was intermittent or if it always happened after syncing with iTunes.
Perhaps the 'manually manage music' setting refers to things done to the iPod from within iTunes - such as stuff like putting music/playlists etc manually (as oppsed to syncing) onto the iPod (from within iTunes), rather than creating on-the-fly playlists on the iPod when out in the wilds far away from any iTunes.
Maybe the older iOSes had the iPod-created playlists as temporary only? (Never tried it in iOS6, I stayed on a lower iOS, and have yet to try it on my new 5G and iOS7).
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PS - VoluptuousYak, you might want to consider getting some 'iPod to Computer' software so that you can safely get all your music back onto your computer as backup in case anything happens to your iPod! There's a few good programs out there, though I'm not up on the latest and the greatest.