I have two JTVs. I have them both at the most recent software level as of mid May 2015. I have experienced the phantom drop D tuning on one of the JTVs multiple times. I have to power it off to get it out of drop D. I had it happen during a gig and at first thought the bass player was Fing up. then I realized I was in drop D and was trying to switch patches and switch back, messing with my tuning dial all while attempting to sing and play. I should have turned off the modeling and used the pickups. Instead, I muffled the string that was formerly my low E. After the song, I powered off my HD500, unplugged the variax and powered everything back up.
Since multiple people are experiencing this, it seems like a bug.