Ok, i experienced Protean changing my opponents Greninja into Water and Dark after using Scald and Dark Pulse, respectively, but he also used Spikes, but didnt turn into Ground.
I assume he remained a Water type because my Rotom's Hydro Pump was resisted, when it should have been SE.
Finally, the message "The opposing' Greninja's Protean made it the Ground type" DID NOT appear, the turn he used Spikes.
As far as I know, Protean works with Status moves, as i have previously became Poison while using Toxic Spikes.
Replay of Protean-Spikes-Ground bug:
http://replay.pokemonshowdown.com/ou-141718804