D string issues

I'm having an issue with my D string where it sounds dead, and creates a chord sound when hammering on a fret. What I mean is, I'll hammer a note and the buzz will create two distinct sounds, like a chord. One, the note I'm hammering, and another note that's caused by the buzz. The dead sound accompanies any fretted note or when played open.

I just replaced the strings and the dead sound is still there. Also, I hear what sounds like rattling coming from the bridge saddle. I checked it to see if it was loose or messed up or anything, but it looks fine. What's going on? Any ideas? It's a MIM Jazz, if that helps.

 

I think maybe it is the nut slot. I don't think it's an issue of the action since it only happens with the D string. I've compensated by adjusting the height on that one saddle and I still get the same results. Bummer.