In my personal opinion, the interaction with iTunes has never been perfect or even desirable with regards to playlists. I have my iTunes set to manually manage music and videos, so that when I get a new song I can just drag and drop instead of doing a full sync. Today when I drag and dropped Rihanna's new song onto my iPhone, iTunes thought it would be appropriate to delete the playlist I just took 20 minutes to make because the genius feature is so effing horrible at creating good playlists.
Can anyone answer WHY iTunes does this? It's extremely annoying.
Hm. I've never experienced this. I also manually manage my music, but I normally just make a new playlist and select that from the iPhone sync page. I'll try to check it out. On another note, I haven't thought to even check and see whether iTunes-->iPhone is still garbling my smart playlists...