I have this issue as well, looks like a bug with the new match service found a work around on the Apple Forums that works every time...
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Select a song to play in Music (must be a song downloaded to the iPhone, not streamed)
Once it starts, close Music (home button)
Kill Music (app launcher)
Restart Music (will open to the song you had playing before)
Atomic symbol re-appears...
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Couple of quirks
Only works with songs on your iPhone (not iMatched songs)
iMatched songs do add to a genius playlist once there (very strange)
Genius lists made on my MBP show up through iMatch, but are not refreshable
Genius lists I make on the iPhone are refreshable....