So I don’t know if this will help, but I recently updated to Yosemite and ran into the same muting issue today as I was editing. Same thing – If I mute, it unmutes when I press play and vice versa, but if I mute/unmute while playing it sticks. For an unrelated reason, I decided to sync my settings with CC server (under the Premiere Pro CC menu header on Mac), and when I did it asked me to log in (not sure why I was logged out – maybe due to upgrade? But that’s a different annoyance.) Once I was logged in, the mute buttons started working as expected.
It’s one of those things where the problem is solved, but I don’t know why.
Side note: I had also experienced the missing waveform bud mentioned elsewhere in this thread, and that seems to be gone now, too.