is this auto-playlists or static playlists?
and thats the only thing thats reset?
Looking at the places the flag is set, I cant see how that could be the case unless the playlist file isnt completely saved eg. turn off machine without it being flushed to disc, but then i would expect the entire file to be corrupt when its next loaded.
If you are certain it is a happening then i could create a debug version to trace then places but i will give you some time to see if you do find a pattern