I had a rattle that was driving me nuts on a Tex Mex strat.... It only seemed to happen when i played g and a notes oddly enough.... The starnge part is it sounded like it was coming from the bridge area..... Even putting my ear on the guitar's body it sounded like it was somewhere on the body.. Turns out it was a bad tuner..... The A string Vintage Style tuner was buzzing with some notes and not others... It was hard for me to find that one! Played a big trick on me! Replaced tuner and i'm pretty happy now....
I always put foam in the trem spring cavity to stop them from ringing out..... i know some say that is part of the Fender sound but i don't like it.....
have you checked to see if the truss rod is loose? if it is just give it enough of a turn to get it to stop making the noise but not to affect the tension it has on the neck. i had that problem the other day when setting up my strat....a strage rattle that turned out to be the truss rod being a tiny bit too loose.