A quick Google search found this at an Ultimate Guitar forum:
"Flea occasionally uses a pick; songs where he's used a pick have included Don't Forget Me, Parrallel Universe, Fortune Faded and part of Snow (Hey Oh)."
I stopped following RHCP by the time any of this stuff came out, so I can't confirm. I DO remember him on the cover of Bass Player mag with a headline reading "He plays with a pick!" among other things...
Thanks. It's possible I even have that Bass Player magazine. I will check.