In Jimmy Johnson's thread(s), he remarks that occasionally he gets a rattling E string at the bridge. Not anywhere else, but rattling at the saddle. I had this myself, and thought I'd never track it down, until I just happened to touch the string at the saddle, and that snuffed it. JJ advises to detune down to loose, twist the ball-end a half-turn in the tailpiece and tune back up.
He thinks it's caused by the multiple windings in BG strings, and the way strings can actually twist as they're tuned up.
This may not be what you're hearing, but easy and quick to try.
J o e y